Send link to a document/draft instead of attaching it to mail

In my experience, the key concern about attachments is not the amount of space they take on the recipient's computer (most people have big hard drives these days), but whether they will cause your message to fail to be delivered.  There are two issues that I frequently encounter in which attachments cause problems with email:

Most mail servers have an upper limit on the attachment size they will allow.  At the moment, this is often seems to be no more than 10MB, but I've encountered as low as 2MB.
Aggressive protective software sometimes gets upset about attachments, especially known malware vectors like zip files.

If you trigger a filter like this, your email will disappear into a black hole and, depending on the configuration of the system that ate your email, you may not even know that this has happened. Thus, for any attachment above about 1MB or of an unusual type, I recommend sending a link instead.

Note, however, that links can also be viewed as suspicious, by either software or people, since there's a lot of nasty phishing schemes out there.  Thus, I recommend not using link shorteners and if possible hosting an academic institutional server or on a well-known and semi-trusted service like DropBox.


What information should the speaker transmit during the title slide of a conference presentation?

I've heard the following advice: When the people in the audience see somebody they don't know, they'll be asking themselves "What kind of guy is this?" for at least some minutes. I guess anybody does this, mainly subconscious. This implies that it is harder to convey technical information in the first minutes, since people work subconsciously to find out who you are and what they should think of you.

So when I start my presentation I always have at least three sentences that are not technical. This can be "Thanks to the chair for the (nice, warm) introduction.", "Thanks to the organizers (I prefer to give names here) for having me here (at this nice place/great session).", "My name is...  and I will speak about...  (collaboration with...)...". There could also be a sentence about the meeting in general or one that relates the talk to previous ones at the conference.

This may cost you one or two minutes which you loose for your precious technical content, but I think it's worth it if at least a few people in the audience don't know you already. If you don't spend these few sentences, the chance is higher that you'll loose these people from the very beginning. Anyway, conferences are (in my understanding) as much about people as they are about research. If I go home from a conference and didn't have had nice conversations and met a few new people, it wasn't a good meeting.


Is it normal to find unknown work during peer-review process?

It's unfortunate when a referee points out crucial papers you missed in your literature search, and hopefully it won't happen too often.  (The more you talk with other researchers, the more chances you have to learn about these papers earlier in the process.)  However, it's certainly not abnormal.  Nobody can be an expert in everything, some references are really not easy to find, and sometimes you just miss something for unclear reasons.  If you publish enough papers, it's pretty much guaranteed that a referee will occasionally point out something you wish you had known about earlier.  This is one of the advantages of peer review.


Do researchers make more mistakes as they continue to work in a discipline?

I think it's not that you're making more mistakes (not that I know 100%, to be honest) but that you are becoming more aware of the subtleties of your field, and are therefore becoming more aware of the difference between, say, a well-studied, published researcher and yourself.  As you learn what is and isn't important, you start to recognize that you need to be more precise and rigorous.

The best advice I have for you is to take note any time you make such a mistake.  Why was it made?  Was it because you just wanted to write something down andget through it?  Was it a genuine misunderstanding?  Was it because you understood exactly what you meant, so you assumed that others did too?  etc.  Then, address the individual causes.

One of my biggest issues was the latter - I knew what I meant to say, so I didn't bother to be careful defining my terms or the context.  It was obvious to me, so I forgot that I had spent months figuring it out and therefore it wasn't obvious to anyone else.  I took a long time to remind myself that a proper setup  is extremely important in selling the relevance and impact of my work.  I still make that mistake sometimes, but I'm at least more aware of it.


Answering "Why are you applying to our university?"-type question in the statement of purpose

We want to know a) if you did your homework about us, much as you would for a job opportunity, and b) if you actually are a decent fit with our departmental culture as well as our academic specialties.

Not doing even the most cursory of homework (reading our website, looking at our faculty expertise, checking out a student group or two) suggests you just aren't that interested in us -- either you're flailing or you're spraying applications everywhere in sight. Neither of those suggests you will do particularly well here.

The academic matching isn't quite as critical for us (though this will vary quite a lot from department to department). In our discipline, it's quite common for learners to change niches during the program, and that's fine. We're mostly concerned about a severe mismatch, that is, you are strongly interested in something we have little or no strength in.

As for how much to say, this is where an admissions essay differs from a job cover letter. The essay is actually about you, not us! You can express sufficient and suitable interest in us in a sentence or two: "I look forward to studying X with Professor Y, who writes so well about Z" or "I appreciate your strong commitment to Q, a commitment I share and hope to expand upon" will do fine.

I'd lay off the "nice location" if I were you; it comes across as backhanded negging, as though the location were the only thing we have going for us. I won't say this would eliminate you from consideration (where I am, we really do have location going for us!), but it would raise a possibly-offended eyebrow or two. If, however, "nice location" means facilities the department has some control over or works hard to fund and maintain (such as excellent lab space or over-and-above digital capacity), that's fine to mention.


Applying to Ph.D. programs in history when my degree is in a science field

This depends on your institution, but most likely, yes you will need to have a certain undergraduate background. History is a field that requires a background, and this will be needed for PhD studies. Nevertheless, as you do have a science degree, I believe that there are programs that will accept you into terminal M.S. programs where you can then apply for a PhD. My advice - look around, email faculty, and apply.


My university has three campuses. Two are very close together, in the same town in fact (about a 10 minute walk apart). Most of the main university buildings are on the larger of the two, with the smaller one containing a few department buildings (e.g. Law and Business) and another library. The third campus is halfway round the world in the Southern Hemisphere.

To the best of my knowledge, you can study for a degree on any of the three campuses and your degree will only state the name of the university, not the campus you studied on (which is only of administrative importance and not relevant to what you studied). You even state this yourself in your question:

  "...you get the same degree as the partner University students."

I would not worry about the value of the degree if studied for at a separate campus. The university itself should ensure that academic standards are maintained across all its campuses, including those abroad, as if they did not this would only devalue the degrees they offer.


I graduated back in 1984 with a BSc in Computer Science. Went back for a MSc by research 25 years later, in 2009. Finished that in 2011, and now I'm doing my PhD.

Will you be doing an MSc by research? If you're the sort of person who likes learning things on your own, I'm sure you'll find it easy enough to adjust. Reading scientific papers is a skill that takes a while to learn. (Writing them, even more so!) You can use Google Scholar to search for papers in the are you're interested in. (Many articles will be behind paywalls, so you probably can't access them until you start, but many articles will be freely available.) Expect it to be tough going at first, so don't get discouraged. Also, I hope you like (or at least don't mind) writing, because in many fields an MSc thesis involves a lot of writing.

If you're doing an MSc by coursework, I don't have too much advice to offer.

Your experience in industry will help you a lot. You'll probably have more resiliency than your fellow students, due to your life experience. This will help you deal with stress. You'll probably find that teachers and students are asking for your real-world perspective, which is great for your self-confidence. Also, you probably have a very clear idea of why you're doing an MSc, which will help you stay focused.


I was in industry before returning for a PhD (in neuroscience). I don't know that I regret it, but I do often wonder what my life would have been like if I stayed in industry. For me, one determining factor in returning to school was that I didn't enjoy working on other people's questions. As a software developer, I was always solving the client's problems. As a scientist, I was working on things that interested me (and my advisors).

Factors you might want to consider:

If you decide not to attend, how upset will your future advisor and school be? Will you be burning bridges?
Could you work for a few more years (maybe saving some money) and then decide to get a PhD?
The salary for a CS PhD is generally not that bad. It is not the same as being a penniless undergrad.

I think you should talk to your advisor and let them know how your are feeling. That will give them a chance to provide advice, and also gives them a heads up that you are having 2nd thoughts (which seem totally reasonable to me). If they react badly (which they might do), that is a sign that this relationship might run into trouble anyway over the course of the degree.


Is creating your own "experiment" considered cheating during a physics exam?

No, this is perfectly fine. In physics, it is common to see students making odd motions as they think through the problem or apply rules like the right hand rule. The usual caveats apply: you must not be distracting or obnoxious, must not broadcast data that other students could use to cheat, and must follow all announced regulations.

Yes, like with anything else, there are a million corner cases and caveats and unreasonable proctors that we could have fun trying to anticipate -- but I suggest we find more productive ways to spend our mental energies.


History MA Thesis: Advisor wants my research sent to her

Unless you have some evidence that the professor engages in improper conduct (stealing the student's work), I suggest that you give her everything she asks for. There is no downside to this if the advisor is honest and helpful. The most likely explanation would be that she is trying hard to keep you on track and wants early warning if you seem to be wandering.
You may not think this is necessary, and it may not be, but some students do wander and lose focus.
So, assuming a good and fair advisor, sharing can shorten your path to success.
But, if you have evidence that she is not a good actor, you should find a way to work with someone who is. Bad actors are rare (I hope) but they do exist.


Protocol for writing a recommendation letter for someone you only know on a personal basis

Graduate admissions panels are not (generally) looking for personal references. They are looking for academic references.

Tell your friend to find another letter writer; nothing you say about her wonderful personality will help her get admitted. At best, it would be a wasted opportunity for her to submit an actual academic reference; more likely, it would actively work against her (looks like she's clueless, or such a bad student that she can't get anyone to write an academic letter for her).

Also see Kisses of Death in the Graduate School Application Process, page 2, "Harmful letters of recommendation," subsection "Inappropriate sources."


Well, I think few people make a lot of money doing mathematics unless they are "quants" in stock investments, or actuaries in the insurance industry. People don't normally go in to mathematics for the money, but, rather are driven to do it by some internal inescapable mechanism.
My advice, such as it is, is to evaluate your options. It may be that finishing is the best option now, as it shouldn't be far off.
Yes, academia is in a bit of a mess now and the post doc merry-go-round is pretty destructive, but many people in the past have also finished their degrees in terrible economic times. My advisor had just started his studies when the Russians came over the border into Czechoslovakia and shut the universities down. He was delayed for years but did well (after escaping later). I graduated into an economy with no jobs for mathematicians. When we landed on the moon, funding for science and math dropped off a cliff after years of growth. More people had already been hired than could be justified in the new world. I had to take a job at a very low level college, though some thought I was one of those "most likely to succeed" types (My mom, anyway). I also had to change fields to CS and was only able to make partial use of my math skills. But I survived and eventually it worked out.
But, someone who can do mathematics can do a lot of things that require analytical skills.
Your advisor seems like a resource. I hope you are using that to advance. She may not need to worry about her own future anymore, but I hope she worries about yours and her other students. I assume that she has a circle of collaborators with whom she is in contact. If you aren't part of that circle, you need to become part of it. Have her, for example, get you invited to give talks at other places. Right now your advisor is your chief mentor, I suspect. But as you move on, look for others willing to help you advance.
Build your own circle.
And, publish or perish isn't universal, though it is at top places. And it isn't so terrible if you really like to write papers. You are down now, but you want to make your trajectory and exponential one. Once it gets better it will continue.


Respected researchers giving imprecise or misleading explanations in casual conversations

There is nothing strange about this. Not everyone is good at translating the very technical problems they are working on, without advance preparation, on demand and at a moment’s notice, into a polished speech that a random person they encounter (mathematician or not) will find understandable. I think the correlation between what you observed and the quality of this person’s work is essentially zero.

As for the fact that you found his description “misleading” because his papers suggest he usually works on other topics: well, he may be trying to do new work in an area he hasn’t worked on before. This is often my situation, and my own answer when people ask me what I’m working on (especially if the question is posed in the present tense as in your description) will occasionally have little or nothing to do with anything I’ve published.


What is a tutor in Australia (UniMelb)? Is it like a TA? What are the responsibilities?

In Australia, a tutor is typically a casual academic staff member who runs "tutorial" sessions for classes of undergraduate students (typically 20-30 per one-hour class). Tutorial sessions form part of undergraduate coursework, however attendance may or may not be mandatory depending on the course and institution.

Tutorial sessions are normally used to review concepts covered in lectures, go through practice questions, or sometimes students use these classes as a place to collaborate on assignments.

Graduate students can apply to be a tutor for a particular course subject to availability (number of existing tutors, number of students enrolled, etc.). The best way to enquire would be to email course coordinators well in advance of the start of semester to enquire as to whether positions are available.

The pay rate for tutors varies widely, but it would normally be in the ball park of $40 - $100 per hour. The high section of the pay range (e.g. being paid $100 for a one hour session) normally assumes you are also spending time preparing material for the sessions.

Contact your PhD supervisor as they may be able to provide advice and contacts to get your foot in the door.

Side note: In addition to "tutors" in Australia we also have "laboratory demonstrators" who guide groups of 10-20 students through hands-on laboratories. If you are a STEM major you may be able to get a position as a laboratory demonstrator as well. These positions pay less than a tutor, however are more widely available.


Putting off PhD for a (potentially) better experience

It seems like you've laid out the pros and cons pretty well; only you can weigh them. But here is my analysis:

  I feel my academic interests have little overlap with many others in the lab.

In my mind, this is the only valid con. It is difficult to do good work if you are not really interested in the project and don't share your advisor's goals.

  The lab is very young (not sure if pro or con). In the start of Fall 2020, the oldest lab members will be the 2 students in their third year.

I see no real problem with this, given your positive comments about the PI.

  I fear that a rushed and partially-remote PhD will be a lower quality PhD.

By the last year(s) of your PhD, working remotely should not be a problem. 3-4 years in CS does not seem rushed if you already have a master's.

  I would like input on potential pros/cons that I am missing, other options, or perhaps even weighing in on what you think the right decision would be.

I think a missing pro is that you start right away. First, you don't know what the future holds; as they say, "A done PhD is better than a perfect PhD." And second, even if you had a guaranteed perfect PhD starting in three years, this means that you are delaying your professional life by three years. That's a long time -- only you can decide if it's worth it.


Is it possible to continue a PhD program in a different university (PhD transfer)

In the USA it is a fairly common practice though normally a student follows his adviser to another university rather than runs away from him. I'm not so sure about Europe (the rules of the game are somewhat different there) but in any case you should make a few inquiries: first, you should talk to the graduate program director (or someone equivalent) at the place you intend to transfer to about whether they currently accept transfer (or any) graduate students and on what terms (the answers may vary dramatically from one university to another) and second you should contact a potential adviser to make sure that it is fine with him/her (I guess you do not want to start it all over again because otherwise you may just as well wait 3 years where you are, and not everybody would be interested in reading and correcting a thesis on the topic given and supervised by somebody else). Normally, if these two key people give you the green light, the rest is fairly routine (again, in the States).


What to do with an application question when I honestly don't know my plans?

Correct me if this doesn't apply to your case but applications generally provide one or several areas where one can explain their interests and future plans (e.g. statement of purpose). Thus, I doubt that this question is all that important. It might even just be used for administrative purposes within or outside the department.

My take on this is that - so long as you are completely honest about your intentions/uncertainty elsewhere in the application - fudging/randomly choosing your response isn't that big a deal.

So what option should you circle? I would go back and reread the program/department webpages to get an idea of graduate placement. (It is also completely legitimate to ask for past placement if it isn't posted.) If most people go on to grad school, circle yes. If most don't, no. So long as you don't feel like you're lying as you circle, nobody can fault you. They should have provided a "don't know" option in the first place.

Finally, I'm not a big fan of the "NA" response because (a) the question is, in a sense, applicable to you and (b) it may raise unnecessary red flags.


How to deal with anxiety and depression after being kicked out of PhD program?

Seek clinical help! The fact that you are here means that you are someone who believes that you need the help of others and that is very respectable. The problem is that this community, with all the good people in it, is not a good place to provide the help that you can actually benefit from.

In your question, there are a few points that are important. Suicidal thoughts are always serious and must be considered seriously. Failure is not easy to bear and nobody can say that they can have a good time failing their goals but normally, people do not think of self-termination when they fail. If you are having this thought, please seek help.

Also, you mentioned that you have failed multiple times in your life before. If the number of these failures is a lot, maybe you are suffering from some underlying problem that is inflicting your performance. Conditions like anxiety (as you mentioned), depression, ADHD, ... can have a drastic negative impact on performance and the sad fact is that in many cases, people who suffer are not aware of it. If this is the case for you, look at the bright side of your situation which is the potential of finding the root cause, elimination of which can improve your life dramatically. Again this is something that can only be confirmed with the help of clinical professionals. Please seek help.

Remember that failure is hard but also remember that even Einstein failed to procure an academic position many times so it happens and it happens to everyone. As Churchill once said:

  Success is the ability to go from failure to failure without losing your enthusiasm.

Give it some time and move on. That is the most important part.

I repeat myself; please consider the fact that self-termination thoughts should be considered very seriously. Based on your country of residence, conditions may differ but nevertheless, accept the fact that, in any country, there exist people who are trained to provide the type of the help that you can benefit from. Please find them.


Would this be considered a valid reason to apply for deferral for graduate school admission?

You can ask the program what their policies on deferrals are, but I wouldn't defer for this reason.
Your goal at this point is to move to the next step. You've been admitted to a PhD program, so you completed that transition, it's time to start working towards your PhD.
It's perfectly reasonable to finish up previous work as a side project (you don't want to delay progress on your PhD, but it's worth dedicating a bit of extra time to polish up a manuscript and get it through review). Assuming your start time is fall 2021, you still have several months to push the project as far as you can. I would strongly suggest that approach rather than trying to buy another year, even if it's permitted to do so (it may not be).


Is it OK to mention a two-body problem during a tenure-track interview, if getting the job would actually resolve the problem?

There are really two ways people can take this:

"If we extend this person an offer, he will actually accept." This is what you are hoping for. This can be good, especially if you are "too good" for the place you are applying to, where people might wonder why exactly someone with better prospects would choose to apply at a lower rate institution. Then again, it can backfire - if the institution assumes you would accept their offer for unrelated reasons, they might be less generous in the package they offer (pay & perks).
"So... he only applies here because of his spouse?" This would be bad, or at least suboptimal. People might wonder whether you are really committed to working there. If choosing between two candidates whose portfolios both match what the institution is looking for, people might lean more towards someone who doesn't "need" his spouse working close by to apply.

I subjectively believe people will more often have reaction 1 than 2. So this argues for disclosing your motivation. Then again, note how this can reduce your possibilities in negotiation.

To be honest, I'd try to wow people with your experience, portfolio and all-around wonderfulness and keep this aspect below wraps. Unless people ask point-blank: "Would you really relocate from Europe to the US?" But that would likely come up later in the application process than in the initial remote interview.

I looked through Workplace but didn't find anything related. You may want to think about flagging your question for migration there - after all, similar considerations would also pop up for non-academic job seekers.


Does IEEE accept a previously rejected paper for peer review?

If it has sufficient changes and answers the concerns of the editor you will probably get a new hearing.

However, if you think of it as the same manuscript then perhaps you haven't made sufficient changes that it will be considers as new, rather than a resubmission.

However, if you have done the necessary work, I think your note accompanying the manuscript (NEW manuscript) should be sufficient. It is a courtesy to them so that they can be reminded of the history.

And of course, make sure it doesn't read like a "report". You may be able to get some local advice on that.


Thinking about leaving industry job and taking up a postdoc

I am in a different field (maths), but I know the stories of several people who went to work in unrelated industry jobs after their PhD, only to decide after a few months to return to academia. It never seemed to have hurt them, but there is of course a danger of survivorship bias, as I never got to know those who failed.

Since it does not seem like you actively burned bridges but only declined offers, I would simply approach the professor with a bit of humility. You made a mistake, but you are willing to correct it and six months is a short time in academia anyway. To add to that there is less danger of losing you to industry now than there is for a post-doc who hasn't tried it yet.

Concerning the "dark side" jokes, with most people they are merely that, namely jokes, so I wouldn't worry that much. They didn't really move away from you, you did move away from them. After all, with you in industry, there were simply no more research collaborations to be had and less of common interests.


Does one typically hand over their research work to their lab if they decide to leave academia?

Ideally, all work would be carefully documented and discussed with co-workers in the group before someone leaves. Often times, though, departures are much more sloppily handled.

However, the research group obviously retains an interest the lab notebooks, data, and other work products created while someone is part of a research group. For data retention practices, I would say that "best practices" would include leaving the originals with the research group, while the person who created the data keeping a copy for their own personal records later down the line.


Is a MOOC "degree" worth putting on your resume?

I (a professional in the field of computer programming) would treat a MOOC "degree" as equivalent to "Continuing Education", but not equivalent to a degree or other accredited education.  If it is:

Relevant to the position/grant applied for or the paper being submitted
Substantial; not an introductory course, but sufficient work to suggest meaningful learning
Recent; in the last few years at least
The only education/experience you have in that area

Then I would consider putting it on a resume, but not directly along with education.  I would put it in a separate section, after the education, something like:

Additional Relevant Endeavors

Completed certificate in Machine Learning, [MOOC], [Date]; explored different methods related to Machine Learning, such as k-means clustering, Neural Networks, and applied logistic regression, using Matlab and R.

That provides enough information to give the reader an idea of what you did (so they don't have to look up the class) and an idea of why you put it on there (let's say, you're applying for a grant using Neural Network Algorithms to find a cure for cancer).  You include it to show you have some concept of Neural Networks, which is not otherwise shown by your experience or education.

I would generally not include MOOC certificates, though, unless it was truly important to the application (ie, filled a significant and relevant hole in your education and experience).  Certainly in professional circles this isn't going to buy you much, and I suspect in academic circles it will buy you less.


How does one change to engineering for graduate school after undergrad in a science field?

I will answer a slightly more general question.  How does one change fields between undergrad and grad school?  The answer very carefully is correct, albeit unhelpful.  The single most important criteria when applying for a strong PhD (at least in math, engineering, or the natural sciences, but probably true in other fields too) are letters of recommendation and demonstrated research ability.  Bad grades can sink your application, but good grades (even from a top school) are not enough to get you in (nor good test scores, although they help).

If you want to get a PhD, but don't have any experience in the area, you should first apply to a masters program, where you can gain experience and impress potential letter of recommendation writers.  Often admission to a masters program is less competitive than to a PhD program (if even getting into the masters program is difficult, you could start as a non-degree student).  But if you can publish a few papers during your masters and convince a few of your professors that you have both the ability and desire to succeed in grad school, then you're application to a PhD program will be much stronger.  I also recommend that you talk with the schools where you plan to apply and ask what they suggest that you do to strengthen your application.

You might also like to read this question and answer Is it possible to attend graduate school in pure math after undergrad in CSE?


Controlled publication of an efficient factoring algorithm?

You can prove that you have the algorithm without publishing it by publishing the factorization of a large number of well known test cases. Then people have time to adapt to a possible threat. If you are afraid of the government or the mafia, there is a sufficient number of ways to publish the algorithm at a preset date in the future, from cron jobs to hidden messages to good old notaries.


How do I know if I'm unprepared for my math PhD?

The fact that your adviser thinks you're doing fine, in particular, suggests to me that you may be dealing with some impostor syndrome.

I think when most of us start out in PhD programs, we feel like everyone around us is doing much better.  Like they all belong here, but we don't.  This is usually accompanied with a feeling of "I had better keep my head down and stay quiet, so no one notices I don't belong here and kicks me out."

You don't say much about your conversation with your adviser.  Hopefully it was an honest conversation about why you're concerned.  As long as it was, consider trusting that they know what normal looks like.  You might also want to talk with some of your classmates more - you may be surprised to find that the ones who seem to be endlessly more successful than you are feeling identically.

PhD work is usually a whole new level of difficult, so it's not necessarily a warning sign that you feel like you have to study for hours to get anywhere.


Common basic information and research for journal club presentation

PaulV's contribution is excellent.  In addition:  Understand the context that the paper appeared in, i.e. try to understand why the author wrote the article.  See the article in its historical context.


How to write an abstract for a summary paper based on a longer paper?

First, write a new one without looking at the old one.  Then, compare the two and see if you missed anything.


How to deal with an advisor who wants a "friendlier" relationship with me than I do?

I don't know if a meeting at which you "set the agenda" would be particularly helpful at this stage. It might make him feel "attacked", put him on the defensive, and he may retaliate against you in response. (I'm not suggesting that he would try to get you kicked out of the university or the department; there are many, many other small and large ways an advisor can make things difficult for a student. You already suggested that when he's mad at you, he deliberately ignores you emails, for example.)

I strongly disagree with the advice to flaunt a (real or fake) relationship, to let your advisor know you're unavailable. I've seen people try this, and in my experience, when applied to someone who does not respect boundaries, the outcome is often that then he starts asking you a whole lot of very uncomfortable questions about your boyfriend and the relationship.

Also, he's probably doing this because he enjoys it (flirting, the chase, whatever), not because he wants an actual committed relationship. So I'm not convinced that he would be dissuaded by your unavailability.

Instead, I suggest you start using a variation on the following phrase to respond when he does something that makes you uncomfortable:

  I don't want this. This makes me really uncomfortable.

As in,

  I don't want you to take my photo. Please don't ask again, it makes me really uncomfortable.

or

  I don't want to talk about my personal life with you. It makes me really uncomfortable.

etc.

And, if he persists in whatever is making you uncomfortable,

  I need to go (get a cup of coffee/make a phone call/talk to another student before he leaves for the day/make some photocopies/etc.)

then remove yourself from the situation.

I recommend practicing saying these words on your own, until they feel natural. This will help you feel less flustered when a situation comes up.

I also concur with StrongBad's suggestion:

  I would suggest the OP writes down every time she tells the advisor he made her feel uncomfortable. She should also keep track of times he makes her feel uncomfortable in which she was uncomfortable telling him he made her feel uncomfortable.

and I would add, also make a note of who else (if anyone) was there at the time.

This will help in two ways:

You'll be able to tell if the situation is getting better or worse with time.
If you do need to escalate at some point, you'll have some documentation.


Taking my research idea outside my paid job

If the idea is valuable you should talk to an attorney.

You want to avoid encumbrances.  If there is some small chance that if the idea hits it big, A can claim some ownership, the thing to do is to get a letter stating that A waives all claims around this idea.

There are also time-sensitive issues surrounding your situation from the perspective of protecting IP.  In your conversations with A and B, you might have "disclosed", starting a clock starting for patent procedures.

Again, if it's important, this is what lawyers are for.


How should I reference my Github repository with materials for my paper?

Such resources, especially if they are a supplementary to the paper, i.e. in some sense a part of it, should be referenced in a footnote and not in bibliography.

Do include not only the URL but also a short description; and do try to keep that URL valid - once you publish that link, it's frozen forever.

It also helps to include the opposite citation. In the readme file of that library, include full citation information of your paper. This will allow others to gain extra information about the methods, and also give you citations if/when others build upon your work.

Some publishers also support binary attachments for supplementary information. If they do, you should use it - prepare a package of the current stable version and upload it there. It allows for reproducability, as a specific version is referenced which relates to the actual paper, and not some improvements done in 2020 that change everything; and it also attaches all relevant information together with the paper at the publisher's site, which will stay valid even if that github repository goes away for whatever reason.


Ethics of a potential collaborator removing another researcher from a project?

There is nothing unethical about this.  You approached a researcher with an idea for a future project, which you both agreed would be a good idea.  However, your employment situation makes it impossible to meet the potential collaborators entirely reasonable demands.  (I would probably not get involved in any research project in which I could not, in principle, have access to the underlying data.  I might never need to see it, but if there is some kind of problem, I would definitely want to be able to look at the raw data for myself and draw my own conclusions.)

Having suggested the research project but been unable to come to an agreement about how it should proceed, you are in a tricky situation.  The other researcher has no obligation not to pursue the project without you or your employer.  I would not consider it a particularly friendly thing to do, but there is no ethical problem.  Your original idea should be acknowledged in the final publications (or whatever) based on this research, but that is as far as your contribution may go.


Is it reasonable to leave a PhD if your supervisor leaves the university?

First thing: There is no such thing as "PhD transfer". (At least in Germany.)

I don't know your university, but is the cases I know, you do not start any official PhD in the first year, but only later. Usually, you make an agreements with some advisor about the PhD thesis, working contracts and so on, and sometimes you enroll as a PhD student, but in most cases there is no official file at the university (but this may change in the near future…). At some point (where I am, usually in the last year) you fill in some form with which you start the official process of graduating (Eröffnung des Promotionsverfahrens or something similar).

So, if you haven't started the "Promotionsvorhaben" formally, you can quit and start new at any point.

More practically: You should discuss your options with your advisor. She is the right person for this. She may have suggestions how to proceed, e.g. she knows people who would like to take you as a student, she has a direct line to these people and will get a response quickly. She may help you to judge the possibilities that you have at the university where you are and she may also know you, your strength, and your preferences already.

Finally, I find the notion of "important university" a bit odd. There are some universities in Germany with a bit more overall prestige but there also also many not-so-well-known universities which are top at specific fields. So, the university name does not mean too much.


How many external reviewers is typical for a tenure case?

The actual number varies by institution and, frankly, does not matter that much.  The real questions are:

Are you known in a community?  Do people in your academic community generally know of you and, more importantly, your work.
Does the university want to keep you?  It is always possible to find people who will write either effusively positive or cynically negative reviews of anyone and everyone.  Such reviewers are generally known to people who seek their reviews.

The first question is loosely tied to the visibility of your research, and the second question is loosely tied to your value within the university (often including teaching, grant funding, collegiality, and the like).


Move from my current university or stay with a longer term proposal?

Noöne but you can make this decision, so here are a few thoughts that sprang in my mind when reading your description. I hope they can be of help in your decision-making.

It looks like your option #1 is more of a gamble (which might be a pro or a con depending on your own character!). It seems that you would go to this new group and change your research topic: if so, you have to realize that a one-year position is quite short for learning/adapting to a different area of research. I think it's good for a post-doc to actually pursue something different than he did during his PhD, but it is more risky on a one-year contract.

Second thing: if you go option #1, would you be burning bridges with your current place? Or would they welcome you back after your one year of US experience, if you don't find another post-doc in this new (sub)field? If you think you can pretty much fall back to option #2 in one or two year's time, then option #1 sounds a lot less risky.

Finally, being a rather “independent” post-doc (i.e. working with a professor who's not fully involved) has some advantages if you can handle it and find intellectual support in other ways (collaborations, conferences, visiting positions, …). It allows you to establish yourself as an independent researcher, which is a first step to become a group leader yourself.


Received an email from potential advisor and my name was wrong. should I correct him?

In case the email was actually intended for the other person, it would be courteous to reply, saying that you got an email from him that you think may have been meant for someone else.


Is the professor allowed to force all of his students to retake the final

There's nothing illegal about it as far as I can see, so we can get that out of the way first.

As to fair, if there are still regularly scheduled class days, they can be used. If the exam is available online originally and planned to be made online again, then given a large enough testing window to account for other exams, I don't see a huge problem.

Now, if for whatever reason the exam would need to be retaken on campus or during a specific small window of time that students may have conflicts with, then the most logic solution in my mind is to make the final optional, or to cancel it all together.

However, the professor will have a fair amount of freedom to decide how to deal with the situation and will undoubtedly have consulted with their department head to make sure the solution seems reasonable (at my university we have to get our dean to approve any exam time outside the standard exam schedule). As a professor, I would personally consult with the department head if for no other reason then to give him a heads up on something that has the potential to generate academic grievances.

If your friend feels the solution is unjust, they should begin an academic grievance process, which will be outlined in the student handbook or similar. The first step is normally contacting the professor to discuss the issue.


Is it a good practice to indicate the desired handling editor when submitting a paper?

I would only do so if you have a very good reason to want a particular editor (or to avoid another one): while there can exist valid such reasons, it could also be a warning sign for editors. For example, if you ask that the editor not be the “usual” editor for your particular subfield, it may be regarded as you trying to avoid careful scrutiny. So, if you are not asked about it, and you don't really care (or trust them to make the right call) (which should be the majority of cases), just don't do it.

Regarding usage: most of the chemistry journals I know allow you to pick your handling editor directly from a list (although availability and workload management might lead to changes after submission), and some journals allow you to pick both preferred and non-preferred editors.


Why do potential supervisors not reply to my emails?

I don't know if this applies to you, but it might help: I receive quite a few e-mails from prospective graduate students. I am looking for new students, but I delete most of the e-mails that I receive without reply. My reason is that most of the e-mails are obviously form letters that are sent to multiple professors with no indication that the student knows or cares about my own research interests. If they didn't spend the time to assure that I might be a personal match with their interests, then why should I waste my time replying?

I don't know if this is your case, but I do recommend that you spend the time (up to 30 minutes per professor) to get to know their research interests based on their websites and their publications on Google Scholar. Only e-mail people whose topics seem similar to yours. (This might eliminate several professors.) When you do e-mail, one paragraph is all you need: you just need to explain directly to the point how the professor's research interest match your own.

Of course, I can't guarantee that anyone will reply you if you do this, but when students do, I always reply them and enter into a serious e-mail exchange. Actually, even if the student's interest doesn't actually match mine (or they pointed out an old research area that I no longer pursue), as long as I see that they made a sincere effort to know my research (again it takes up to 30 minutes per professor), I always at least give them the courtesy of a reply (though I can't guarantee that anyone else might).


Contacting potential advisers before deadlines

It is definitely helpful to contact potential advisers for many reasons.  In my experience, one important reason is that a professor for whom you would like to work may not have space or funding for you.  Sometimes those things can be overcome, and sometimes they can't.  If there is only one professor whose research interests you in a given department, and that professor isn't taking students for some reason, that could make your decision for you.  It's not a pleasant situation, but I have seen it happen several times.

You might also find that, after talking to a potential adviser, the focus in their research isn't quite what you thought it was.  Of course you can find that out by reading the recent publications, but a conversation can also be enlightening.  They might tell you about one or two specific projects you would likely be working on, and if those projects don't interest you, you might want to move on.

If things look like they could work out, it is still an excellent idea to stay in touch.  If someone on the admissions committee gets to know you somehow, that will really set your application apart.  The chair of the graduate admissions committee at my undergraduate institution even told me that, more than once, he has admitted a student simply because he or she was calling or emailing and expressing real interest and desire to become a student in the department.  Don't be annoying, but a couple of emails and/or a phone call or two never hurt anyone.

If there are several potential advisers in one department, that is great.  It likely means that department focuses on research that interests you.  Don't be afraid of getting in touch with more than one professor.  The more people that recognize your name, the better.  Just be sure to be polite and respectful and leave a good impression.

Good luck!


co-authorship of the unresponsive and careless advisor?

This is a common dilemma in academia that can quickly escalate to sorrow. My advice is short and straightforward: once the manuscript is ready from your side, politely approach your both supervisors and ask them directly about their expectations concerning authorship.
I understand the situation may feel uncomfortable and you'd prefer to make this decision relying on everyone's best judgement, but most of the times supervisors are overly touchy regarding merit and authorships.

Thread carefully there and be frank with your superiors. Good luck!


Using public profile data from website for research

What you're describing is the OKCupid data release, just without publishing the dataset. Note that the OKCupid "study" and similar studies on Facebook data were considered ethically controversial by some, who argue that users who participate in a website are not necessarily giving consent to participate in a research study, especially when users' profile data is only available to logged-in users. (Also see: “But the data is already public”: on the ethics of research in Facebook by Michael Zimmer.)

Re: avoiding a lawsuit, you should get the OK from the website. As Wrzlprmft pointed out in a comment:

  Unless the research could cast them in a bad light, they may be interested to learn something about their userbase as well. Also, you may get to know relevant information about the data, such as hidden selection mechanisms or similar

If you choose not to go that route, I'd recommend consulting with a lawyer re: the website's terms and conditions. Realistically, nobody here can tell you the likelihood of being sued, or of losing the lawsuit. A lawsuit would probably be based on the terms and conditions of the website; get a lawyer to review them. Your colleague's assessment that they "don’t explicitly prohibit mass downloading of information" is not exactly reassuring. (For example, language in the terms and conditions that enumerates the permitted use of the website can potentially exclude other uses, without explicitly enumerating the prohibited uses.)

The case law on this issue is far from settled. The decisions so far have been limited. There is no legal precedent that clearly establishes that "scraping is always allowed if the T&C don't explicitly prohibit it".  There are some select cases that have begun to map out cases where scraping is and is not prohibited, but the legal territory is not yet fully explored. Some further reading on case law in the US and EU:

Judge: Google cache kosher when it comes to copyright
Judgment in Ryanair Ltd v PR Aviation BV
Judgment in Innoweb BV v Wegener
Web Scraping in an Era of Big Data 2.0


What's the etiquette for a short visit to a US university department by a faculty member from another university?

I think you are the person who would be invited out to lunch, dinner etc. as you are the guest :) ! However, there is nothing wrong with inviting your opposite number to talk in an informal setting. The only consideration is that you know the lay of the land!

Depending on how many days you would be spending at the US university, you might want to make a strategy on conversations and prospective collaborations.

I am assuming you would have results to show and tell and with a punchline at that. That generally helps.


Is there a risk of sharing my idea with other researchers via e-mail?

There is always risk. You may have come up with the greatest idea your field has ever seen, that would tempt even the most honest of researchers.

The more salient question is "Is there a major risk?"

And for that, I'd suggest that the risk is fairly minimal. If you have a senior mentor, you can minimize it further by asking if they have recommendations for who you might get in touch with. But if it is genuinely just a question - to be frank, it's likely not worth stealing. Ideas are, in and of themselves, a dime a dozen. There are things these researchers are working on, interested in, have funding for, etc. And there are likely more of these than they have time for. For example, my planning board has a massive pile of projects I'd like to do that vastly outnumbers the projects I'm actually working on. I'm not going to add another because a random person contacted me and I decided to steal their idea.

There's also a risk in not sending it - that your idea remains undefined, and you lose the potential for the input of experts in the field. I'd consider that a much greater risk.


Would giving a talk in a colloquium aid my application?

That depends on the graduate school, and the competition. So it is hard to say. However, giving talks is part of the day to day life in academia. So getting practice early won't hurt once you are in the graduate school.


Whether it is during your interview, or when they read you SoP, there will always read your enthusiasm between the lines. If you happen to be doing some self-study by yourself, it clearly shows that you are personally interested in the subject and enthusiastic about it.

Plus, by doing undertaking such projects, you will have a much wider perspective about the field and you will be familiar with more complex ideas. So, when they ask you "why do you want to work on this field", you can give a much more specific answer than "I find it interesting".


Tools to assist with upper-division grading?

It seems like Gradekeeper remains the go-to program. So if you want to do something more sophisticated you probably want to think about working up some macros in Excel. For example, this post has some good example macros. There were three extensive discussions of gradekeeping software on Profhacker that you might want to skim. One on gradekeeping programs in general, one on a neat iPad app called GradeBook Pro and one that focused on a few cloud based apps for grade keeping. None of these seem to really do what you want, and with any of these you probably want to talk to someone at your institution about any policies they might have, particularly for something like a cloud app or an iPhone app regarding where student grades are kept and FERPA.


Thoughts on Business Ownership Experience in the Academic CV

I like your compromise proposal.

It is important, when writing a CV, to demonstrate knowledge and respect for the process by which you're evaluated. In my mind, that strongly suggest putting the "standard" stuff first.

But I also heartily endorse your decision to highlight your work experience. It sounds quite impressive, actually. Just do it after you have assured your prospective employers that you have the credentials and skills they're looking for.


One principle is that the instructor should aspire to grade in a way that results in the grade being most closely correlated with those aspects of the knowledge and skills being assessed that the instructor considers important.

As an example, it is a common belief among instructors of university level mathematics courses that exam questions should test conceptual knowledge rather than facility with arithmetic and other low-level calculations. For this reason, most instructors would take off only a very small number of points, or not take off any points, for a small error of arithmetic in an otherwise conceptually correct answer. However, some instructors might consider accuracy to be an important skill to test in and of itself, and may impose a heavy penalty of points for even small arithmetic errors. So you see, the grading function chosen by the instructor reflects that instructor's view of what's important. Decide in advance what's important to you, and grade accordingly.


What should I do if someone is claiming my research on ResearchGate?

I think the most important part of your question is the bit about "with the same name".

ResearchGate has very loose and rather questionable practices in how they manage their citation data, which tends to err on the side of inclusion.  Moreover, their terrible user interface makes it very easy for somebody to do things like click "add all" and end up with a whole bunch of misattributed publications.  In the little bit that I played with ResearchGate before giving it up as basically useless, it kept offering to give me authorship of papers by people with the same last name---not even the same first name.  It will also automatically add papers to your profile in some circumstances.

What I'm driving at is that, given that you and this other researcher have the same name, it's plausible that they didn't even do this intentionally and have just written off the whole ResearchGate mess.  The fact that they didn't respond to your direct email is more problematic, but again not necessarily damning---you may well be going into their "headache pile" or even their spam folder.

Given all of this, what I would suggest is a two step solution:

If you think you have standing to do so, send a DMCA takedown notice to ResearchGate: it's fast, easy, and might get the content taken down.
After that, just start ignoring the whole mess.  It's not worth your time and energy.


Is it possible to get a Ph.D. position in Europe after a one-year diploma?

You are eligible for a PhD in some European countries with just a bachelor's degree. There may exist countries - e.g., I believe Germany -* where a master's degree is universally required before a PhD. In other countries, requirements vary between institutes (and supervisors may even insist upon their own requirements). So a list of countries probably isn't useful and exceptions would no doubt exist.

* A comment clarifies that a master's degree is not a universal requirement in Germany. Another comments notes, "it might not be possible to employ the PhD student as a scientific employee (Wissenschaftlicher Mitarbeiter), which is the default for PhD students in many fields," so, for practical purposes I presume a master's is a widespread norm in Germany.


Can anyone write a paper and then publish it in a journal?

In principle: Yes, of course!

No journal I know has a rule that requires a minimum level of education or a specific affiliation. But in order to be accepted for a journal with reasonable reputation, there are several requirements:

Contribution: With more education (not necessarily a higher degree) it gets easier to provide a better contribution. As you said, just waking up with a great idea without even knowing the fundamentals of the field of research before is unlikely.
Novelty: For an external person it is hard to decide if he has really found something new or he was just reinventing the wheel. That is much easier if you are part of the research community. That does not necessarily require any affiliation, but for example the regular participation at conferences and workshops.
Experience: You need experience in many areas to write a good paper. A lot of (if not most) papers are rejected not because of bad ideas, but because of wrong experimental setups, wrong application of statistical methods, ugly looking plots that do not provide confidence intervals ... and most importantly because the paper was not written in a convincing way. You can not learn these things by just reading a book at home.
Time: Research requires a lot of time! If the university pays at least part of your bills you have more time to do research.
Money: Depending on the journal, publishing might be very expensive. With an affiliation at a university it is easier to find someone who pays for your publication.
Reputation: Last but not least, there are things, such as reputation of the author, that should not influence a reviewers decision, but they do at least sometimes.


Does a PhD student need a co-supervisor?

The direct answer is not a PhD students does not need a co-advisor. The problem here is to think about the role of co-advisors. I am sure the view on this varies so my view is coloured by situations with which I am familiar, which is the US and Sweden. Co-advisors may be involved because they have specific expertise that may be relevant to part of the work, for example specific investigations, lab work ec. Co-advisors may also be there to provide overall scientific expertise and provide feedback on written articles or the final thesis or both. Hence a co-advisor may not be very active when you start your PhD. At the same time by signing up as a co-advisor, I would expect the co-advisor to be open for discussion during your time as a student but it may fall on you to initiate such contacts when you need it. The main advisor is, after all, the one responsible for the direction of your work within your thesis topic.

So while one does not need a co-advisor, there are many instances where such support is necessary or at least very useful.


What can a student who works hard,is motivated to learn do to improve his grades?

I think your difficulty is with prioritizing tasks and committing to them. Don't worry, it is not uncommon, and its easy to solve once you accept it.
First, you need to decide which is more important to you at present, doing well in the exam or learning the subject well.
(Obviously learning the subject well is very important, but the exam grades may be a more immediate and pressing concern. Possibly they impact future prospects significantly, or maybe they are not so relevant). If the exam is important now, then be strategic about it. The deep appreciation of the subject should have started earlier, and if it didn't, you should revisit it once you get through the exam. If the exam isn't so important, then relax and keep enjoying the subject.
Second, about topics to study. A few days before the exam is not the time to play favorites with topics. At that point it shouldn't matter what you like or don't like (again, this is something for either before or after exam week). So spend an appropriate amount of time on each topic. A lot of students spend more time on topics that are graded heavier - this I personally detest, but it is strategic and meets a short-term goal.
Finally, mnemonics and active recall (I'm not familiar but this sounds a bit of voodoo) and the like are probably best left behind in school. I know it takes some pain to change mindset and the way you approach subject matter, but there is a reason university is distinct from school. Sure, use mnemonics when they are a standard tool (colors on a resistor for instance), but don't use them to start committing regular subject content to memory. Even if you have understood the topic well, this will serve as an unhealthy crutch that you'll keep falling back on, and will feel helpless without.
Apologies for being a bit blunt, but one of the distinguishing skills of a university education is realizing that we are responsible for our condition and our actions alone can improve them. Its certainly not late to start seeing that.


How to finish Master's Thesis when my adviser is too busy to help me thoroughly edit what I have written?

It sounds like you have two major concerns about getting quality feedback from your advisor: (1) he's busy, and (2) he's not as familiar with your new topic. I'll address these separately.

Getting high-quality feedback from someone very busy

To get the best feedback possible from your advisor, make sure that whatever you send him to review is as polished as possible. If he's pointing out typos and areas where the writing has issues, he's not going to have as much time to evaluate the content, which is where his feedback is most valuable.

It will also help if you identify and tell him about the areas where you think you most need extra high-quality feedback: "Could you tell me what you think of the formulation in Section 3, I'm not so sure about that part."

Getting high-quality feedback from someone not an expert in the topic

Even though your advisor is not an expert in your new topic, he's an expert in something and he knows what good work looks like. He knows when an argument seems weak and "hand-wavy" and when the evidence on offer doesn't support the claim.  So he's still likely to have good advice even if he isn't as familiar with your topic as you would like.

In fact, for PhD students at least, it is generally assumed that the student knows more than the advisor about the thesis topic by the time the student is about midway through the program.

On crowdsourcing thesis feedback

Having said all that, it's still useful to get comments from others in addition to your advisor.

Ask your friends to read your thesis to (1) find typos and obvious mistakes, and (2) note areas where they think something is unclear, so you can improve the writing. This will help you make sure the version you send your advisor to review is as polished as possible, so you'll get better feedback from him.

If you know some professors who are expert in your topic, you can send them a copy, but follow the advice for getting feedback from someone very busy: Make sure what you send them is very polished, and identify where you want their help the most. If you don't know any professors who are expert in your topic, then after your advisor gives you his feedback, ask him: "Do you think we should also send this to an expert in the topic for review? If so, do you know anybody we could send it to?"


How does a low quantitative score on GRE general exam affect admissions to mathematics PhD programs?

Unsurprisingly, mathematics PhD applicants are rumored to have very high GRE general test quantitative scores.

I found a few links by web search where PhD programs list the average GRE scores for their students. (Everyone, please feel free to edit this to add more.)

Penn State: https://www.math.psu.edu/grad/phd/faq.php
Duke: http://gradschool.duke.edu/about/statistics/mathematics-phd-admissions-and-enrollment-statistics
U Penn: http://www.math.upenn.edu/grad/graddata.html
U Maryland Applied Math and Statistics: http://www.amsc.umd.edu/join_us/faq.html#Tests3
Georgia Tech: http://www.math.gatech.edu/academics/graduate/faqs-graduate-admissions#MINGRE

These sites all show average quantitative GRE score is in the high 160s, which corresponds to about the 90th percentile (which was around 795 out of 800 on the old scale). So, if these statistics are accurate, the rumors are true.

Now, for the more personal side of the question. You asked if the scores are "enough". Most schools have no firm minimum score. If you have sufficiently good credentials, you can overcome the low GRE score. What you will need, certainly, are very good letters of recommendation.

I would include a statement about anxiety in your personal statement, because even if the committee has heard it before, they haven't heard it from you.

You may also want to make sure you have diversified your applications: don't just apply to top-25 departments. There are a lot of perfectly fine schools lower in the rankings, which may not be as broadly strong but which may be strong in particular areas of interest to you.


Completely stuck with nonsensical project

I think you should stick with it.

As far as my understanding goes, publishing 1-2 papers as a mathematics PhD student is (more than) enough to get your degree. It may not rank you as a star but it's a solid proof of competence. Working on other lower risk projects may not improve your thesis significantly. Successfully completing a high risk project, however, will be a boon to your PhD.

Furthermore, this project yanks you out of your comfort zone where you can gradually work towards a solution. Instead, you now have to find one key idea and you're basically done. Again, you've already shown you're a good mathematician inside your comfort zone, so showing that you can solve those kind of problems should not be your main priority.

I think your advisor has a high opinion of you and wants to give you an opportunity to prove exactly how much you're capable of. That's a nice vote of confidence. If you actually do want to stick with it, it's probably a good idea to find ways to enjoy the project. Possible ideas: talk to other people about the project, especially to your advisor and the other two professors. Sometimes spend as much time as possible trying to find a solution even if you feel it may not work. And sometimes work on unrelated fields or do other stuff (such as teaching) that is both inspiring and relaxing.


Many universities have a "writing center" or equivalent that will typically be your best starting point, since it has people who are paid to sit down with you in person and help you solve this problem.

If your institution does not have such, there are massive numbers of online scientific writing courses that may help. Personally, I have found Jean-luc Doumont particularly helpful, and especially his "architectural" view of writing. Different people will find different resources fit their personal learning styles best of course.

Next, if at all possible, make sure that you are partnering with mentors or co-authors who are good at writing.

Finally, read!  The best way to understand what works in communication is to be a reader and learn what works for you.


Is it normal for professors to give credit to their students even when they don't deserve it?

Probably the conclusion that you don't deserve credit is not totally justified. I am pretty sure that the final result contains at least some words from your drafts. On a more serious side, it may well be that professor could never have written the final result without having read your drafts. You know, the first sentence is the hardest, and professors also know how to procrastinate. But they usually often know ways around it! Having somebody else to start the writing process, and giving this guy a deadline (and you know he will make the deadline) and then starting from there is one great way to get started on time.

Actually, in previous days my professor asked me quite often to draft something for him (emails, abstracts, reports,…), but when he got my draft and started writing himself, most of my draft disappeared as well. In fact he even told me in advance, that this will happen, but having some draft helped him to get going.

Writing paper together with an advanced researcher often feels the same. I echo the other answers, that you can learn a lot from carefully studying the edits. And remember that writing the words in one thing, but getting results, sharpening formulations (not sentences) and structuring text is another thing. So just accept that he thinks, that you deserve first-authorship and be happy.


Is there any way to get accepted in PhD program without masters?

In most European countries following the Bologna process, a master's degree is a "hard" prerequisite for being accepted into a PhD program. There is no easy way around this, in large part because the PhD typically encompasses only the research phase of a standard US PhD program. By skipping or omitting the master's degree, one would have a "weaker" degree than someone who completed the master's.

Your best bet would be to find a PhD program which offers a master's program as "preadmission" to the PhD program. Not all doctoral programs offer such master's degrees, but many programs designed to attract international students will.


What are some useful workflows for keeping track of interesting but not immediatly relevant books/articles?

Here are two approaches that work for me. The first is a way to capture the essence of documents that are "very interesting, and may prove useful in some future, as-yet-imagined research project, but not immediately relevant". The second is a way to quickly capture the details of documents and prioritize how soon you revisit them to read in more detail.

First, you can use tagging in your reference manager to summarize the documents. I use endnote. In the research notes section of endnote I put tags to characterize the reference. For example, I will tag the method (e.g., experiment), theory (e.g., motivation) and so on where relevant. Where possible I will also link the record to a specific paper, for example by tagging it as RP1 (RP1 = research paper 1). I separate tags using semi-colons. When it is a paper that I think I will need to read in the future, I will put VIP, or to read. I might also write a note (which I put in notes section of the reference record) of why it is important to read the paper. All of the above means that I can easily find papers with certain tags in the future, as well as use this meta knowledge to quickly determine which papers are relevant on certain topics - without having to actually reread them to find out.

Second, you can also put it somewhere in a list. I use a prioritised to-do list including an an Eisenhower grid, in evernote.

To do today

1.

2.

3.

To Do Asap:

1.

To think about

1.

In my case I have 7 lists in my evernote document. As shown in figure 1 above 2 of these are at the top of the Eisenhower grid: To do today and To do asap. Four of them are within the box: High importance/High urgency, High importance/low urgency; Low importance/High urgency; Low importance/Low urgency. I have one below the box called: To think about. If I find a useful paper I will add it to one of these list so that I can find it at some point in the future. Of course the list I chose to add it to will be a function of its relevance.


For Postdoc positions seeking experts in programming language, what are the expectations and what should my strategy be suitable for those positions?

It was just using an available inbuilt function and wrapping a program around it to serve my purpose.

To be honest, this sounds like the majority of programming that takes place in academia.

Obviously the exact skill requirements will be different for every position, so I can't give you any specific advice, but knowing how to link together existing functions in order to create a program that you want is a useful skill that not everyone has. Don't let your impostor syndrome get the better of you.

Your advisor or someone else in your particular field might be able to offer advice on what skills you should focus on developing.

Background: I recently finished an MA in a field where many researchers are using programming, but also many are not. I have a programming background, but many students with much less programming experience than I have were able to be successful in writing programs for their research.


What are the advantages of writing a thesis with rMarkdown?

RMarkdown allows you to put your code directly into you manuscript and is functionally an easier to use replacement for Sweave.

The same advantages and disadvantages listed in this previous answer hold for RMarkdown as well.

Last, Chester Ismay has created a thesisdown template, which would be a good starting place for you.


This is an unprecedented time in academia, and your best course of action is probably to just wait awhile for your professor to catch up on his emails.

As a professor myself, I have several emails left over from the just-ended spring term that I need to respond to.  My college announced that there will be cuts to staff, which haven't been finalized yet, so it's possible I won't even be employed here next term.  My kids' school and daycare are closed, so on top of childcare I might have a couple of  hours each day to do work-related things.  And I don't run skype anymore since discovering other, better options, so if anyone in my old skype contact list is contacting me, I wouldn't know about it.

In other words, if your professor's work-life situation is anything like mine (and many, many of my colleagues at other institutions, judging by their social media posts), he just hasn't gotten around to your email yet.  It doesn't have any bearing whatsoever on his thoughts about your graduate application.  You've got until July for applications, so give him another week and then try emailing him again with a polite "just in case you missed this" nudge--that usually does the trick.


Taking vacations days in the middle of a semester

In the departments I have worked in, it would probably be considered unprofessional to leave on a pleasure-cruise in the middle of the semester. I suspect that that is universal.

In other words, this is not the image you want to project as someone who will still have to go through the tenure process. On the other hand, it's a fairly small thing -- people are gone all the time, although almost always for professional reasons: at conferences, workshops, for collaborations. So the mechanics of being gone are all appreciated in any department, such as moving classes around, giving out reading assignments instead of in-person classes, or putting a midterm exam on such a date and having someone else proctor the exam. Students also understand these things. In the end, it will be a judgment call: It comes over as "frivolous" to leave for a vacation and cancel classes over it, but it's also not a huge deal and I'd be surprised if anyone would think that you'll lose tenure over it. It's just a bad mark in your peers' perception of your professionalism.


Citation policies: original papers or recent monographs?

Why not cite both?

  The following theorem is due to Doe [37]; see also [28] for a modern exposition and further background.

Here [37] might be Doe's original paper, and [28] the recent monograph.

Math journals rarely have page limits, so there's no disadvantage to including more citations.  This way you credit the original author and also point the reader to the resource you think will be most helpful.


Why ask both for CV and publication list?

On mathjobs, my workflow when glancing through files from candidates is to look at the publication list instead of the CV.  This is for two main reasons:

CVs typically frontload a bunch of information which I already have from the mathjobs cover sheet (education, postdoc, advisors, etc).
CVs are longer than one page, so finding the publications takes some time.  Publication lists have the info I'm looking for right at the beginning.


Editorial rejection: should I write back?

No doubt your first instinct is to challenge this desk rejection, but I would advise against it.

It is well known that appeals rarely succeed when referees go against you. When a handling editor thinks your work is not sufficiently interesting, I'd say an appeal is even less likely to be successful.

Coming specifically to Phys. Rev., your situation is somewhat worsened by the fact that alternatives to the Phys. Rev. A-X stable are not as attractive or popular.

But if your work is sufficiently useful, and helps advance your field, it will get cited even if you take your paper elsewhere. There is evidence for this in your case: You have senior researchers on arXiv giving you good feedback.


How to cite a conference paper similar to thesis topic published during research?

I would probably follow roughly the following steps:

Read the conference paper thoroughly, and decide how it relates to your paper. This part is regardless of the details of who published first; it is just a matter of knowing the facts, and clearly figuring out what their work is about, how it overlaps with yours, and to what extent the results are the same or different.
For results that overlap significantly, determine who published first. You state in your post that you have been working "since mid-2017" and "my research started earlier". To be clear, those details are not really relevant here. The only thing that is relevant is who published first. Fortunately, you are hopefully OK here as it sounds like you have publications in this topic as well.
If the authors of the conference paper could have cited you, but didn't, consider reaching out to them directly. From your post it sounds like they didn't cite you, even though you had already published? In this case, you can send a polite email saying you saw their work, it looked interesting, and asking them if they are aware of your earlier work. You should assume good faith; it is likely that you both completed similar work in parallel.
Write a section on the paper in your related work (to your thesis), explaining how the research differs. How much you say mainly depends on how related the work is, not when it was published. If it happens that the works have some of the same ideas and solutions, you can explain this in a number of ways, depending on the results of (1), (2), and (3):

"[X et al, 2019] also developed a similar solution in parallel to our work."
"[X et al, 2019] have a different idea on how to solve problem P, based on QRST, however, they did not compare with [your name et al, 2018]."
"Some aspects of our solution, including ___, were originally developed in [X et al, 2019]."

While the above are useful phrases to cover yourself from criticism, these should not be the only thing you write, and you should only say these as a last resort. It is much better if the work differs in some way, and you can explain clearly how it differs. Even if only part of it differs, explaining which parts differ will be much more helpful to future readers.

Some other comments:

  So far, I did not cite my own papers in my own thesis (this is what my professor told me).

This is really strange to me. If I were reading your thesis, I would really want to know what papers of yours you are building on. But the culture may be different between my field and yours (I am in Computer Science). Your advisor of course knows best.

  Now, it is not clear when I started doing my research.

As I said above, this isn't super relevant; it's more important who published first, and whether the work was done in parallel.

  And of course, I would like my research to be considered novel in the thesis.

We all would like this :) This is the best reason to have a thorough comparison, so you know how your work differs, in case anyone asks. If it doesn't differ at all, but you did the work in parallel, that may be fine as well. And if you published certain results first, don't be afraid to highlight that in your thesis or if anyone asks you about it.


What is the best way to turn down a Postdoc offer?

Keep it short and honest.

For example,

  Dear So and So, thank you for your offer for a postdoc at Blah. It's
  an attractive offer, but I've decided to take a position at Foo-Bar
  instead. The work you're doing over at Blah is very interesting and I
  look forward to interacting with you in the future.

Of course if you have more than one rejection to send out PLEASE PLEASE don't do it generically. Tailor it to each place individually. It takes a little more time, but it's a fair exchange given that they took the time to give you an offer.


I'm assuming you mean abandoned in the sense defined by the USPTO. A patent (application) is abandoned if the application is never completed for some reason and cannot move forward to registration. In that sense an abandoned patent is not a patent, so it would seem to be a mistake to include it as anything other than incomplete and abandoned work.

Perhaps you can find a way to include the work in another way that is more positive. Did it result in any publications, for example?


Are there any Universities that accept PhD students based on Research Proposals?

If you are asking whether some university will accept you solely based on a research proposal, then I think the answer would be no. You might be able to find an exception of some university-proposal combination that would make it work, but that isn't how it works. Universities accept students into doctoral programs based on the evaluation of a set of criteria that suggest that the student has both the appropriate background and the likelihood of success in the program and thereafter.

Having a proposal is probably a plus, but, in the US, at least, it isn't required, as you note. It isn't likely even evaluated.

However, assuming that you have an appropriate background, then you might be able to find a professor somewhere, certainly in the EU and possibly in the US, who is willing to work with you to advance your entrance into a program. In some places, the professor is even an essential link. But the proposal alone isn't going to be sufficient. You will need to convince people, at a minimum, that you can succeed with that proposal and the result is likely to be sufficiently significant.

However, I think that being too committed to a particular proposal is likely to work against you, rather than in your favor. You need to find an advisor who is either hugely interested in that topic or willing to spend time advising and evaluating something that has less importance to them. Both of those reduce your chances. The latter is, perhaps, more likely than the former. Some professors are happy to have students who need little shepherding and who are self directed enough to get the job done. But I doubt that the majority of people work like that.

So, the bottom line is that you have a chance, but you probably need to be a bit more flexible and you need to attend to the qualities in your background that suggest success.


Can I use my first name instead of last name?

Use a digital identifier such as ORCID - https://orcid.org
It would be impossible to address all the different naming conventions so you can distinguish yourself in every subgroup. But with ORCID, it would be easier to track your publications and work compared to sifting through your duplicates on google or a database.


How can I pass my PhD thesis defense when nothing has been successful?

The specifics here are certainly best discussed with your advisor. They should know about your discipline, and how to frame results in a way that is suitable for the community.

  Has anybody done a "fully failed" PhD defense ... and passed? How would one do this?

For me, it does not sound at all like you "failed" in your PhD. A PhD is a research project, not a product. Ultimately, you (and your committee) should not evaluate your results based on whether they ended up being useful, but based on whether you had a reasonable thesis and a thorough scientific study of this thesis.

That is, if you proposed a novel approach, collected reasonable data, and thoroughly validated your initial thesis, your research was successful, independently of whether this approach then ended up being used in the larger project context. Sure, it would be nice to be able to say that your approach has then helped these other people to do A, B, C, and D, but the real world does not always work like that.

To me, it is mainly a question of mindset. If you yourself consider your PhD "failed" you will have a hard time selling it to a committee. You need to embrace the idea that you did good research, and not measure the success of your own work on factors outside of your control. In that sense, you should defend what you did and why. You can, and maybe should, discuss why it ended up not being used if there are interesting lessons learned, but stay away from political or interpersonal arguments (these can indeed sound whiney). Stay positive and focus on what you did, not on how much other people then liked the results.


Why would the conference organizers ban the inclusion of new links (e.g. to datasets or repositories) in the text of the rebuttal?

The underlying reason might be that rebuttals should not present new data/results which were not included in the original submission.
Presenting new data/results in a rebuttal is problematic because it increases the review load: The new data might require some detailed explanations of how they were obtained and how they add to the overall work. Effectively, the reviewers have to discuss two versions of each paper (without and with the new results). The organizers might want to avoid that, given that the review load at good conferences is normally already quite substantial.
Of course, one could still allow links if they don't present new data/results. But this raises the question why these links were not included in the original paper. Potentially there have been previous experiences according to which the risk of misusing links to refer to new data/results is seen as too large.


Could I get into a C.S. Ph.D program after an undergraduate from a totally unknown school?

The reputation of your previous program will be relevant when applying to PhD somewhere else. However, this by no chance eliminates your chances of getting into a good PhD program if your CV shows your competence compared to other applicants from other schools. In other words, in cases where the schools (and probably professors) are not well known, having publications in internationally reputable venues (not easy to do in undergrad) along with good standardized test scores might carry more weight than school-related attributes such as GPA and maybe even recommendations. (These will still matter, but less so when compared with GPAs and recommendations from highly known institutions/professors)

I will add this however. Being in a small and newly-established program can have other potential drawbacks. Assuming that a new and small program equates to less experienced professors and less budget, you will be missing out on the higher quality mentoring and availability of the required labs and equipment. Also, the student body will also be smaller, so you will have less chances to find people to collaborate with and share ideas. These drawbacks can be just as bad as the perceived reputation of the school for PhD admissions.


How can you determine whether a journal is indexed in ISI or SCI?

International Scientific Indexing (ISI) has a list on their website. The same is valid for the Science Citation Index (SCI). You can search for journals by title.


Are there integrated software solutions to support that?

Beeminder integrates with Github or Bitbucket, so if you keep your Latex or Markdown in either of those, you can automatically gamify your writing without having to do any manual data entry.
Beeminder is a commitment tracking service that plots your progress towards your goals, like this:

(image source)
There's also negative reinforcement: if you consistently fail to meet your goal, you "fall off the yellow brick road" and you pay actual money. Beeminder is good at tracking your progress without punishing you for small temporal variations in productivity.
In this context, your goal would be to make a consistent habit of adding to or editing your thesis.
With git integration you can set goals like "N commits per week" and data points are added to your Beeminder graph automatically when you commit.
There's also integration with Draft, if you prefer to count words edited rather than commits.  I haven't used Draft myself, but it looks like you can use it to write in Markdown.


Is there a particular structure that a research lab should have?

No, there are no standards for what is considered a "lab."
I know of labs with many postdocs, lots of staff, and few students. I know of other labs that are more focused on undergrads, with a few grad students and no postdocs.
Of course, you can take the lab composition into account when deciding whether it is a good fit, but there is no criterion to point to and say "ah, this is a poorly structured lab."


What should raise red flags to detect fabricated data

There is only one reliable way to do it, which is to try to replicate their results.

The unreliable, but not completely useless way, is to see if the numbers fit Benford's Law.
Benford's Law describes the distribution of the first digit of many very diverse data sets. This is the distribution:

(public domain chart from Wikipedia)

Andreas Diekmann describes this further, in Not the First Digit! Using Benford's Law to Detect Fraudulent Scientific Data, a paper in the Journal of Applied Statistics from 2007


What to do when you get a grant and move to another institution

And in particular this goes for H2020 projects.

This happened to a colleague of mine for FP7, I assume H2020 will be pretty much the same. Essentially, you have two options:

(1) Find a proxy to formally finish the project on your behalf. That is, find somebody at your current institution with a high enough status that he is allowed to take over the project without much administrative quabbles (e.g., a senior professor), and formally hand over the project to him when you leave. You will of course still do the actual work - the handover is just a formality. Of course this requires a significant amount of trust and goodwill (on both sides), so you better be good friends with the person that proxies for you. As long as you both are at the same institution, the administrative effort of this solution is not too high.

(2) Officially transfer the project to your new institution. This requires an amendment of your DOW (description of work), and the sanctus of your new institution, all partners of the project, and the european commission (i.e., of the PO and the responsible lawyers on EC side). This will take long - expect the entire process to take possibly a year or so. Additionally, there is a chance that some negotiations between you, your old institution, and your new institution are required (e.g., to answer the question to what percentage the overheads should be transferred to the new institution). H2020 proposals are good money for universities, and you should not expect your old institution to let go of such a project easily.

Edit: Clearly, option 2 is only available if your new institution is also eligible for H2020 funding.


Authorship change on conference paper after conference program is printed

I have very little experience with "talk only" conference papers (and, as jakebeal correctly asks, why is it a paper if there is no paper?), but generally, the ordering of authors (or even who is an author) of a conference submission has very little to do with who prepares the presentation or who actually does the talk.

Rather, the order on papers is usually either alphabetical or by some measure of "who did the most work" for the actual research that is being presented. Hence, a change in who presents a paper (which often happens, due to time constraints, visa problems, illness, ...) usually does not require a change in the order of authors, as the underlying work (and who did it) has not changed.


Is it generally worth the time and effort to challenge incorrect exam test items?

Though the fact that I, a student, was the only person who realized the mistake and sought to have it fixed reflects very poorly on the quality of the institution.

Yes, it does.

  I believe the material should be correct so that future students do not suffer the same frustration nor are taught improper concepts.

Of course it should.  But ultimately, the correctness of the course material is the responsibility of the instructor, not your responsibility.

  I have had to fight tooth and nail to correct some of the material.

That strikes me as quixotic.

It's certainly reasonable, and helpful to future students, to report errors that you find in the course material.  The instructor should then either fix it, or discuss with you why the course material is actually correct.

But if the instructor does not seem interested in doing so, then it's probably a waste of your time to "fight tooth and nail".  Unfortunately, crappy courses and instructors exist, and it's not your job to fix them all.  Simply quit giving them your money and attention: look elsewhere for better courses.  If you like, leave negative reviews.  Future students would be helped by having the errors fixed, but if the courses are as poorly managed as you describe, they would be even better off not taking them at all.


Congratulating professor to having moved to a new university?

If your relationship was all one-way, as professor-student relationships often are, then I would not mention it.

If you sometimes had casual conversations that made things more two-way, and you happen to know something that provides context to this move (for example, if this is a solution to a two-body problem, or you happen to know that the professor was hoping to move to a certain geographical region, e.g. to get in more skiing or hiking or snorkeling, or to support an aging relative) then sure, you could include congratulations.


Manuscript status changed to editor assigned after under review, what could be the reason?

The first mission of the editor is to assign reviewers and take a decision depending on their return. Hence the first Editor Assigned to Under Review. The reason with it is now Editor Assigned can be due to several reasons. This depends a lot on the manuscript management system, and the editorial practices.

Either:

The editor has already received the necessary  reviews, and is taking a decision (perhaps taking another look at your paper)
The editor has not received the necessary reviews.

The second case may be caused by different situations. Even with a "minor revision", it may happen that:

not enough of the first round reviewers have responded. Some journals impose a minimum. So he is looking for another reviewer (or doing the review himself), as suggested by @Buzz
the 2nd round raised more than minor concerns. Sometimes, after the first round, a reviewer notices sometimes more important, and can ask for a major revision (or a reject). So the editor may add another reviewer, to settle the case.

The latter happened to me once as a guest editor. ED1 said major, ED2 said minor. After round 2, ED1 said OK, ED2 said reject. A very painful situation  for everybody.

I wish you are just in the editor decision frame.


Does reusing my own code from one project to an other count as plagiarism?

Ask your professors. Your senior project professor/adviser/committee probably has specific expectations about the work they expect you to do, and this is going to vary from university to university.

My feeling is that you'd be OK using this code as long as it was developed for this project and it hasn't been submitted for credit in another class. Even if it has, re-using code from a previous class is not necessarily a bad thing if you can show how the new application is substantially different and worthy as an independent credit.

If your only goal is to avoid punishment then note that many schools have "honesty policies" not "plagiarism policies". It's not enough just to avoid plagiarism, but you must be honest in how you conduct your work. Finishing a project in six months and pretending like it takes you another six months to finish might be just as punishable as plagiarism. Finishing a project in six months and telling the professor that you think you've met the requirements and you'd rather focus on finishing your other classes is not dishonest, although your professor might disagree.


There exist a lot of standards for document/publication types. Here are some examples:

ORCiD work types
Endnote reference types
RAK WB, see chapter 1.2 (a system created for German libraries with a hierarchy for document types)
DRIVER used by DINI (repositories)
...

As stated here, each database might have its own definition, i.e. there are a lot of standards. Before creating a new one, I'd check if one of the already existing standards fits your requirements.

Note: Please feel free to edit this question to add more standards for document/publication types.