Collaborating with professors after graduation

It is absolutely possible in principle. What I wonder in your case is what do you have to make it attractive for the professor? I as the professor surely wouldn't be interested in collaborating with somebody in order to make their profile stronger or give them a better recommendation. What do you have to offer that is attractive for the professor? An idea? Access to industry money? Interesting data or an interesting problem?
I am a statistician and have been involved in projects where I was contacted by people from industry who wanted my statistical help dealing with their data, in some cases with potential to publish together, and/or pay. When I liked the problem and had some spare time for this, I did it. Actually in many places industry collaboration also can make the professor's CV stronger or give them a relevant recommendation letter applying for grant money and the like.
Edit, replying to the first comment: The situation is somewhat different if rather than having something to offer that the professor doesn't have (like data, money, or some relevant expertise in a different field or of the background of an industry project) you want to work in the professor's area on their problems. Personally I'd be rather skeptical of such a thing, because it is somewhat risky to have somebody working for me whom I don't know and who has no contractual obligation to do that, so I may invest some time but finally results/a publication may not materialise.
Note that "the professor's projects" can have various shapes. They may have money, a group and a work plan to which they may be committed (including contractual obligations), which doesn't give anybody from outside the chance to just jump in. On the other hand, they also may have some flexibility to do spontaneous projects (as I can do working on industry projects). I can imagine positive responses particularly in case that you propose something interesting enough that the professor can see your competence and expertise. The prospect of having a collaborative publication with just giving occasional input in quite limited time may be attractive for some. Also there are young researchers who need to build up a better list of publications themselves, without already having research students or a team, who may grab such an opportunity. My subjective probability for getting a positive response would be far lower than 50%, but getting one out of ten attempts or so doesn't seem unrealistic. The best way is maybe to propose something specific related to their interests, and if your letter/email looks good and competent enough for them, you may have a chance.


Just started a postdoc, but it went REALLY bad, REALLY fast. Stay or go?

With all else the same, given an choice between staying in a bad situation that cannot be resolved or leaving it, the decision is easy.

Of course, all is never exactly the same. When the balance is uneven, I hold at the point where you are that following your passions and desire for healthy growth is the most important factor. You can and will end up in situations where leaving has worse consequences than staying and you must therefore resolve the issues at hand or let go (and stay where you are). Is this case really to that point for you? I sense not.

As you weigh the various concerns, realize that you owe the lab only the respect that you will never be dishonest. The promptly, professionally delivered statement that "I am leaving because this is not the fit that I really wanted" is all that is required at the end of the day.


Want to do mathematical physics - if first choice dept not a good fit, can I switch?

It seems like "you" should do a lot more research into existing graduate programs, since you haven't mentioned maybe the most obvious thing you should do: apply to an applied math Ph.D. program.  You should look carefully at what different programs expect, since "applied math" is a slippery concept; however, as such, applied math programs don't have an uniform an expectation of student background as pure math or physics programs.  Interdisciplinary programs are hot at the moment, but unlike a usual math or physics degree, what's on offer will vary dramatically from university to university.  In my new hometown of Waterloo alone, there are (I think usually funded)

Masters in Applied Math (https://uwaterloo.ca/applied-mathematics/graduate-students/applying),
Perimeter Scholars International (https://www.perimeterinstitute.ca/training/about-psi), and
a special stream in the Institute for Quantum Computing (https://uwaterloo.ca/institute-for-quantum-computing/programs/graduate-studies).

That's a bit out of the norm, but there are many other programs out there.


How to move from experimental to computational research

I did a very similar transition, moving from wet lab biology late in my undergraduate career to computational biology, which is what I work in now. It's certainly doable - I made the switch with no programming experience whatsoever.

I don't necessarily know that the desire and knowing some Python is out and out enough to make someone confident of letting you dive head first into their project, but it certainly is enough that I'd ask around. You should be aware that a switch like this will probably cost you some time, but if you're okay with that, see if its possible to do a rotation in someone's computational lab - a semester or two for you to get the feel for what it's really like, pick up some skills, and hopefully either they'll pick you up, or "I did a rotation in Dr. So-and-So's lab..." being enough to make someone take a chance on you.

There are some other things you can do as well - follow your interest in computational work by replicating some classic papers in the field. Doing some side projects - computational representations of your current work, or implementing a commonly used algorithm on your own (say, the Gillespie Direct Method and it's many approximate methods). Things that will build your skills and suggest that you're worth taking a stab at. The other suggestion, if you can't effect a full transition, is to potentially propose one Chapter/Specific Aim/etc. of your dissertation as a computational project, and put someone appropriate on your committee.


How insulated is guaranteed funding from an economic slowdown?

Large universities that are offering guaranteed funds often don't guarantee where those funds will come from, simply because they cannot: the money doesn't exist yet. In my graduate program, this is what guaranteed funding meant:

Your first year was covered on a T32 training grant from NIH. This allowed you to rotate in different laboratories without those labs needing funding for you. The NIH provides these grants specifically for this purpose. If all the training grant slots were filled, some students would be admitted directly to a lab that was able to fund them starting their first year.
After rotating, you would join a lab. This lab would basically need to have funding for you, or else you would have to teach. It is important for students and their PIs to talk about funding, since some labs have new grants or several grants and can pretty much slot out a PhD student's entire time in the lab; others have funding expiring soon and the student and advisor need to have plans if that funding falls through.
At any point, most students would apply for outside funding, and some would get it. Even though funding was guaranteed, applying for and receiving grants looks good for your resume.
Students were required to TA at least one semester; many would TA more if they were interested in teaching or to cover breaks in funding in their labs. Usually these would be negotiated with the students and students could time their TAship to coincide with a low funding period in their lab if necessary.
In rare cases, students in labs that failed to secure funds continued their research with funds from another lab, perhaps changing their research project. The program would consider these hardships when granting the PhD degree, and it might result in a thesis that's less cohesive - that's just part of life.

Note that most of these steps didn't really involve the guarantee, it just involved there already being money around the labs that make up the program to fund students. Guaranteed meant that the program would be your advocate and would find you funding of some sort if other sorts fell through. They would find a way to get you a TAship if you couldn't get an RA. They would ask someone else to give up their TAship for you if they could get funding from their lab. They would find a way to stretch funds from one part of the budget to another to make sure you graduate. They would use training grant money for you to finish your final semester. The money wasn't in a pot set aside for you at the outset, but in the fungible world of money, the university was committing to support you. Guaranteed did not mean you could work in any lab of your choice and work towards any research project of your choosing, but it meant that lack of funding would not be an absolute reason for you to be unable to continue in the program over your first 5 years.

Every program will differ in terms of what types of support are available: TAships, RAships, PAships, fellowships and other funds. Funding guarantees are important, but so are the sources of those funds, and this should be an open conversation throughout the application process.

As raised in the comments, there are situations where even 'guaranteed' funding can be revoked, since the guarantee almost certainly comes with basic strings attached such as continued progress in the program, not violating a code of conduct, etc. That said, this sort of guarantee from a reputable university program is putting their reputation on the line to get you funded. They will only break this promise if necessary or justified. No employer is likely to ever provide you a stronger guarantee.

I started graduate school around the last recession; ultimately, the recession and associated funding cuts meant in some of the years after me the program admitted fewer students than typical over a couple years, but no one went unsupported.


I used a solution that I happened to already have on my laptop on an exam. Did I cheat?

I would say no, unless this was explicitly prohibited beforehand. Look, what's the purpose of a test?  To gauge the extent to which one has comprehended the material. The fact that you did the work indicates you do. Hell, the fact you did it on your own for fun deserves recognition.

What's the point of re-doing the work while sitting in class during a test?  Worse yet, suppose you did and made a mistake due to nerves/time pressure.  You still did and comprehended the material, thus you pass.

Others will disagree, but in my mind, I just want to know if you do or do not understand the material.


In my area the standard is always to have a single methods section; journals would not accept an alternative format. That might not always be the ideal arrangement for every paper, but it's simply the norm.

So what to do when the methodology is somewhat convoluted, or very key to particular elements of the results? Add some "reminder" description of the methods in the results. Keep the fine details only in the methods, but address what you are up to to keep a good story in the results. Minor repetition isn't a problem and helps your paper flow.


Is it valid in the sense that it is likely roughly correlated with the prestige of a journal? Probably. Does anyone actually use the Scimago rankings? Not that I'm aware of. There's a general consensus about what the very top journals are in mathematics with a general consensus that Journal of the American Mathematical Society, Inventiones, and Annals of Mathematics, and Acta Mathematica (not to be confused with Acta Arithmetica) are probably within the top 5 or so, and Annals is probably the most prestigious.

Curiously though, looking at the Scimago rankings, the Annals isn't listed in the top 50 even, and while they have Inventiones and JAMS near the top, their top 50 also includes journals I've never heard of in specific subfields like "Swarm and Evolutionary Computation". They also don't include some decent journals at all on their list. So the upshot is I wouldn't read too much into it. If a journal is in Q1 it probably is a better journal than if it is listed in Q4, but even that doesn't seem conclusive. Talking to mathematicians is probably a better way of getting information about how prestigious a journal is than paying attention to these rankings. And certainly mathematicians don't normally talk about or pay attention to the Scimago rankings.


Travelling for an academic seminar with a 36*48 inch poster board on a flight

One common option is to print or create the poster on a large sheet of paper and carry it in a poster tube.  After you arrive at your destination, buy a blank poster board, and paste your paper onto it.


Get in touch with potential PhD supervisor without a topic? How specific should I be?

From your question, it sounds like you have an area you are interested in, but are not sure what your exact hypothesis or research question should be. For a pre- or early program PhD student, this is normal.

From my experience with PhD programs, students are often pushed to have their exact research question from the first day, but this is not usually not ideal. For most students (as it should be), your research question will change as you learn more about the topic. So, theoretically, how can you be so sure that a research question is the right one from the start without a serious review of the literature (which usually happens during your studies).

That being said, one way to approach this is to ask the professor to coffee or a brief meeting and tell him or her, "I am very interested in your area of research. I do not know enough about it to have a specific research question in mind, but I am very interested in working with you so I can learn more about it and develop my own area of study."

Your question reminds me of one graduate student who was placed with me and was interested in criminology and health, but not sure how the two should intersect. He was very interested in the topic of HIV/AIDS. I'm a gerontologist and he was placed with me because a more suitable advisor was on sabbatical. He learned more about gerontology and ultimately changed his research question to be about aging prisoners, which is a really hot topic. He is doing well. You will figure this out, too. Good luck.


How are paper authors uniquely identified?

Aside from ORCID (which by far not every paper and person has), there really is no sure-fire way to uniquely identify an author. Using the name becomes problematic with common names (not unusual anywhere in the world, but a particularly common issue in Asia) or name changes (for instance in case of marriage). Combining with affiliation and e-mail address will also only get you so far as most academics tend to change universities at least once or twice in their career, and both affiliation and e-mail address tend to change in these cases.

For bibliographic research, the most promising approach is probably to combine all of the above with field information (e.g., a Markus Huber publishing in medicine is not particularly likely to be the same as a Markus Huber publishing in philosophy), and train some sort of heuristic classifier. Clearly, false positives/negatives will happen, but if your goal is to holistically assess a larger field of research a few false categorizations are unlikely to impact the overall picture too much.

If your goal is to assess an individual researcher, really the most accurate information is usually to trust what information the researchers themselves maintain (e.g., a CV or publicly available publication list).


Should grad students also serve as lab managers?

A couple thoughts, on someone who has been now a grad student, a lab manager, and a PI:

Someone has to deal with those things, and the PI is often not the best person for that particular role. And it tends to be helpful if there's a single point of contact for things like "Have we ordered more X?". I find that "It's everyone's problem" turns into it being no one's problem.
A lab that will volunteer you for something while you're not there, the PI can't gauge your workload, etc. is not a lab I'd be enthusiastic about working in long term.
Working as a lab manager is a helpful entry on your CV, especially if you don't necessarily want to be a PI. There are often questions on this site about research careers that aren't TT faculty positions. Lab managers are one of those positions, and having experience with it etc. is a good thing.
It's also a good thing if you are interested in being a PI. Because from experience, when your lab is N = 1 people and you're just setting things up, knowing how all of that works is handy.
"...we're there to do research." And how will you do that without the equipment necessary for your work?

That being said, in an ideal world I wouldn't want a graduate student as my lab manager, because graduate students are inherently transient, and one of the values of a lab manager is as an inter-generational knowledge base. But maintaining a full-time, permanent position for essentially a staff scientist is often out of reach of even fairly well-funded labs.


I have career gap after bachelors degree and irrelevant work experience. How do I write SOP for MS admission in US?

Unlike employers in industry, I believe that graduate admissions committees don't care if there are gaps, irrelevant work experience, or changes of direction in your employment.  Their sole concern are your credentials and capabilities to do academic work.  You should focus all your attention on communicating your skills and capabilities to do Masters-level Computer Science work.  This includes your course grades as an undergrad, your GRE scores, your computer experience in industry, your recommendation letters, and your engagement with professional and academic communities.

(Business schools are probably an exception to this.  Work history is probably important to getting accepted in an MBA program.)


Should I accept a funded MS offer, and then wait for other offers, knowing that under the resolution I can submit a resignation of the funded offer?

You haven't said where you are applying to. While not a law, the offer you received would be in violation of the CGS resolution that offer should be until April 15th. Most universities in the US are signatories and follow this practice.

Regardless, there's no reason to tell them before March 7th considering that's the deadline they set.

Separately, depending on the sort of communication you've had with other schools, you could ask them if they will be able to tell you before March 7th to simplify your decision-making process.

The CGS resolution exists precisely so that people won't be stuck in this position (among first offers of funding).


How to choose an associate editor for my manuscript?

The question boils down how to effectively choose the associate editor and assign my paper to him?

The associate editor (AE) has to first decide if the paper is worth reviewing for the journal (they can often do a summary reject if the quality of the work is low). If it is, they then have to select the reviewers for your paper, get the decision from the reviewers, and then use that to make a recommendation. So, ideally you'd prefer someone who is:

familiar with your area and work,
familiar with people who would be good reviewers for your paper,
someone that you or your co-authors get along with.

Getting #1 is hardest - most journals don't have AEs in every sub-area of a field. As an AE I often handle paper that are in related fields so I know of possible reviewers, even if I'm not an expert in the field myself.

For #3 you can't have someone too close to you (e.g. someone that a co-author regularly publishes with), and you also don't want someone with whom one of your co-authors has very poor relations (e.g. fundamental disagreements about the field).

Note that while you may recommend an AE to the editor when submitting a paper, the editor has the final say on the AE that is selected for the paper.

With regard to your other questions:

  Is it possible that wrong choice of associate editor can lead to rejection of paper?

It is always possible (eg if the AE doesn't like the line of research or chooses poor reviewers), but there are many factors that can lead to the rejection as well, and it is almost impossible to control for all of them.

  Or is it possible that even if I choose an associate editor who is
  not an expert in my field he may send my paper to the appropriate
  associate editor?

The editor may do this if the AE is busy or if the editor thinks that someone else can handle the paper well. It would be more rare for an AE to  ask for a paper to be sent to someone else.


Research Design Help: Measuring the effects of plagiarism intervention

I am just improvising on the fly here but does Korea have software like TurnItIn which measures (in a few different ways) the level of plagiarism in a particular paper or a set of papers usually from online sources.

If you do, then you could think about devising an experiment where, in a class, you inform the students that you will be trying to reduce their "plagiarism tendencies" and take a pre-test perceptions survey. Next, you set a particular class paper as an assignment and note the different measurements on TurnItIn (or equivalent). Then, you make your intervention (in whatever form you choose) and finally set another class paper as an assignment and note the different measurements on TurnItIn this time. Finally, you set a post-test debriefing and follow up survey.

I think this would make for a very nice repeated measures model (from the TurnItIn or equivalent data) and some nice latent variable analysis from your surveys.

I hope this helps you in some meaningful way.


What is the etiquette in using honorary names in the title of North American professors?

These are called named professorships. If you put that term in a search engine you will get explanations from many schools.
Typically, a large donation is made to fund the named professorship or named chair. The name can be the donor or someone the donor wants to honor.
The person who gets the named professorship is selected by the school. It is often already a faculty member or can be somone recruited for that specific spot.  It comes with prestige of the name and additional resources.
Since the OP examples are Cal Tech, here is what they say about it.  Note: this press release was not from the year that either OP example was listed.

During the 2018–19 academic year, Caltech recognized three faculty members with the Institute's most distinguished award for individual faculty—a named professorship. This honor provides faculty with additional funds and resources to pursue their best ideas while they continue to mentor future generations of leaders.

Each named professorship brings its own distinct legacy. Many professorships, for instance, have long-standing histories and pass on through each appointment a tradition of discovery and exploration from one academic generation to the next, from one colleague to another. A professorship may also provide a faculty member with an opportunity to forge meaningful connections with the philanthropists who provided the donation that made it possible.

So the answers are 1. No and 2. Not applicable to an individual taking a name, but the donor would want to have the prominent person’s assent or his or her estate/foundation/relatives’ assent.


Is it a good idea to pursue a PhD in Singapore as a European student?

About point 1, it probably depends on one's field but Singapore is a nice place to graduate from. I really enjoyed the department there and working there in general.
About point 2, it should not be the only reason to do a PhD there but Singapore has a unique feel and is a very enjoyable experience in itself. As anecdotal as it may sound, the food is cheap, eclectic and very good.
A few caveats :

While life itself is kind of cheap in Singapore (eating in food courts is cheap, making your own food slightly more expensive), housing is expensive. You may need to share a flat with flatmates (that can be a very nice experience by the way, especially in a new place).
Having an immigration pass to do a PhD is, of course, not a problem, however your spouse may not get a pass (it depends on your income and I have been told that a typical post-doc salary is below the limit). You might want to check that if applicable.
From what I have seen both in Europe and Singapore, I would say that there may be slightly more pressure on PhDs and  post-docs there than there is in Europe (of course Europe is a big place and it mainly depends on your supervisor).

Obtaining a post-doc in Europe/USA with a PhD in Singapore is not a problem in itself as long as you make sure you meet some professors working in Europe/USA and get yourself invited to some seminars when you're in Europe/USA. That is where the 'large budget for this kind of things' you talk about in the comments will come in handy.


It is very possible that it is unethical, but it would take a bit of analysis to clarify it. Your course professor is probably a good person to adjudicate it. I'd suggest that you take the problem to them, preferably in person.

Using other people's work without attribution is plagiarism.

Go see the prof.


My mum was recently diagnosed with cancer. Should I tell my supervisor?

Many countries have rules in place that allow employees to take paid or unpaid leave to care for an ill relative. No shame or unprofessionalism should result from making a request to accommodate a need to deal with a loved one's illness.

If you have a good relationship with your advisor, then your advisor should understand.

(That said, the advisor may or may not have much control over the viva, depending on who is responsible for scheduling and organizing it, and who else must attend. But you won't lose anything by asking.)


Is it acceptable to ask how a professor would like to be addressed through email?

In contrast to other answers voiced here, to me, signing a mail with {Firstname} is a clear indication that one can address the sender by {Firstname}. It would be unreasonable for the prof signing with {Firstname} to expect otherwise. I don't agree with the "always better to play safe"-advice, as I strongly believe in that an academic discussion should be based on arguments, not on status. If I expected my students to call me in a formal way, then I would have to address them in a more formal way as well (at least, that's what I feel). When I indicate that I as prof feel comfortable with the informal route (which I do by signing my mails in this way), there is no reason not to accept that offer.
Having said that, it is of course highly dependent on culture and language.


When should you publish code on GitHub? Work-in-progress or after publication?

There is a movement gathering strength lately to encourage publishing the code:

Nature-Publish your computer code: it is good enough

Or, more vehement:
If there is no code, there is no paper

The reasons outlied on the article are very reasonable. If you are expected to publish detailed derivations, experimental methods, and proofs of theorems, why would you be allowed to keep the code? No one will accept a theorem if you claim: "the proof is too messy to show, but hey, here are three cases where it works".

I think the best way is to publish the code used as supplementary material, and include a link to the repository, so people can get the improved versions. If you are concerned about people using too bleeding edge versions, make releases, but leave the development public. This will also help you get bugfixes and contributions.

Thank you for wanting to release your code. I really believe this attitude will help make research better.

Edit:

After some time, I have something to add. Most of the code in an application is there for "administrative purposes": load and write data, massage, check conditions... For publishing, that part can be as hackish as one needs it to be. The real "research" is usually in a small part. That is where one should dedicate one or two hours of adding a few comments and clearing the code.

For the rest, a docstring in the functions or a paragraph explaining the aim, should be fine.


There is a wide variety of presentation tools with all kinds of features. However, for an academic presentation (I assume that this is what the question implies, otherwise it is off-topic on this site), animated transitions between slides and, for the most part, on a slide are highly recommended against. The main reason is that they significantly distract an audience from the essence of the presentation, thus, negatively impacting both the audience and the presenter.

When referring to the on-slide transitions above, I said "for the most part", because there are cases, when on-slide animated transitions are actually appropriate and helpful. For example, when a particular slide describes dynamic elements or nature of a system, it is helpful to illustrate the dynamics of changing state of the system's elements or features with animated or otherwise dynamic transitions.

Speaking about presentation tools, most software offerings (standalone and online services) offer the rather basic features that you mention in your requirements. For example, besides Microsoft Office and Libre Office, you can take a look at academically-focused Beamer (very flexible and highly recommended) and knitr software, as well as online services Bunkr, Speaker Deck, already mentioned RevealJS, Prezi (don't like it and don't recommend - similarly to @Nox, I get dizzy from their standard transitions), Keynote (AFAIK, it's Mac-only), SlideRocket and many more. If your subject matter allows story telling (which is what should be the core of ANY presentation, regardless of the domain), but in a more visual way, check Amazon StoryTeller and PowToon.


The correct & acceptable phrase to indicate that some papers are very likely to be accepted

Stating the status of manuscripts in a thesis should not be an issue. The best way is to phrase their status as expressed by the journal. We see this all the time from "submitted to", "under review in" to "revised with major/minor revision". You cannot state that they are likely to be accepted since that is not your decision and stranger things have happened.

What has to be remembered is that even a paper that has been published can be discussed and criticised so the above information just means to an examiner that someone else, impartial, has possibly commented on the manuscript or that a journal has found it worthy of review.

I would guess most examiners would see a status as additional "evidence" for a basic acceptable quality of the work but would not necessarily affect their judgement, which is personal anyway.


Is it OK to reuse part of the related work section published in a previous paper?

Short answer: No.

Medium answer: It can feel silly to find new phrasings for sentences or paragraphs that say essentially the same thing, but the alternative is unfortunately self-plagiarism. You can and should make a comment like "the following subsection is largely adapted from [other paper]", but even with that, the text should be different enough to not be considered a quotation. There is some wiggle room with technical definitions that can't be rephrased without a loss of clarity, but other than that, err on the side of rephrasing.


Do I need to check references of the paper with cross checking softwares?

Overall levels of plagiarism are completely irrelevant. What matters is whether there is at least one clear-cut case in which an extended phrase has been plagiarized from one of the sources. If so, the paper is unacceptable. In principle, one could have 1% similarity and clear plagiarism, or 20% similarity and no plagiarism.

Once you look it in this light, it doesn't matter what the program does with respect to the references. Properly formatted references will look the same in any paper and so duplicating the text of any single reference is not considered plagiarism. (You can plagiarize references, however -- if I were to copy a set of important citations from another paper and then repeat them in order as if choosing them were my own work, this would be plagiarism.)

Of course, plagiarism checking software only catches the most obvious instances: direct plagiarism of blocks of text. One need not copy text exactly to have plagiarized.

Finally, if any of the major publishers have "thresholds", they are being foolish.  As the software producers plainly admit, we are still at the point where a human needs to look at the instances reported by the program and make a judgement call about whether one is dealing with an actual instance of plagiarism.

Edit: Given the comment below, it appears that some publishers are running submissions through a plagiarism detector upon submission. I suppose it might make sense to have a high cutoff above which everything gets rejected as probably plagiarized and not worth the editors' time -- but if they do that, "beating the plagiarism checker" is not what you need to be doing as a researcher. The last thing you want to do is submit a paper that slips in under the threshold yet contains instances of plagiarism that will come back to haunt you later.


Can I use the exact same research proposal for different scholarships?

No problem, often people in your situation do the same. Even professors try to improve failed grant proposals in order to submit it again in other calls.

In your case, I think you must send the same project, since you have already delineated the work you will perform with your potential supervisor and you are just applying for funding. After the results, if both get approved, you will need to choose only one of the grants.

Plagiarism is a completely different thing:

  the practice of taking someone else's work or ideas and passing them off as one's own.

In any case, I think you should talk to your supervisor before submitting.


Why are new encyclopedias being published when there is Wikipedia?

There are a number of specific policies and practices of Wikipedia that reflect judgment calls, and it's perfectly reasonable to treat them differently for different projects:

Above all, creators of another encyclopedia might want to exert editorial control over the product. The rest of this list expresses some of the specific ways they might do that.
Wikipedia explicitly aims to serve a general audience; another encyclopedia might be designed for an expert (or afficionado) audience in a certain field
Wikipedia contributors may be anonymous, and the majority are
Wikipedia maintains a strict egalitarian ideal, which makes it difficult for subject matter experts to exert special authority
Wikipedia's peer review mechanisms are very specific; publishers of another encyclopedia might design them differently
Wikipedia's standards for sourcing, and its threshold for inclusion, are very specific; publishers of another encyclopedia might design them differently
Wikipedia has very specific standards around copyright of text and media

On my connections to Wikipedia: I have been editing Wikipedia (almost exclusively the English language edition) as a volunteer since 2006. I designed the first formalized program to support university instructors assigning Wikipedia composition, on behalf of the Wikimedia Foundation, in 2010. I have run a Wikipedia training and consulting company, Wiki Strategies, since 2009. I have served as editor in chief of the Signpost, Wikipedia's volunteer-run newspaper, since August 2016.


Pros and cons of not having PhD advisor's letter of recommendation after postdoc?

The only time that you shouldn't ask for a letter of recommendation from your PhD advisor is when you are not allowed to ask for one. This is not often the case, but it does arise in a few instances. The best-known one I can think of is that in Germany a Doktorvater (supervisor) is not allowed to write a letter of recommendation in support of an applicant whose PhD he supervised.

Other than that, you should have your PhD advisor write a letter; it is expected by just about everyone that the supervisor will write a letter, and it will definitely raise questions for you if you do not submit such a letter. If there is a particularly compelling reason, then, you should have that well in hand at the time when you are writing your applications. Otherwise, you'll have a lot more explaining to do, and probably a lot of potential postdoc supervisors may not even bother giving your application a second look.


Is it a good practice to choose my undergraduate research topic on my own? Can I get enough help?

So somewhere I've made a moderators life harder, because I thought your three correlated questions were just one question. I think they probably could be, just incidentally. I'm going to answer accordingly, because when it comes down to it, How To Do It, Will I Have Help and What Are the Downsides aren't just correlated - they're interwoven.

My bias: I did my own projects. As both an undergraduate and a graduate student. This worked out quite well for me, but is not without it's pitfalls.

First, yes, your professor should be able to support you in your research interests - the odds of what your interested in being so far afield from their expertise, when you're an undergrad, is fairly unlikely.
That being said, there are two elements of support they won't have: infrastructure and funding. It's helpful, if you're working on a project, for there to be grad students and postdocs working on similar things. Code you can use. Helpful little suggestions like "Have you read Smith's most recent paper in Journal of Important Things?" That kind of ambient helpfulness isn't going to be there. Similarly, even if you're working for free, its way easier to justify conference travel, a piece of software, or an open access publishing fee if it helps an existing research project.

As I said, this worked out quite well for me - I got good publications out of it, and I got to work on my own stuff. But its a harder road, for graduate school may take longer, and you lack the security of working on an established project. Beyond that, if it doesn't work out well, you don't have an entire lab's worth of effort, papers that might be salvagable, etc.


How to avoid authorship drama in this situation?

The explanation is quite convoluted but this looks like a rather common situation: A and B work on closely related topics, both supervised by C.

First an observation:

  While waiting an answer from C, A gets bored and wants to work on his idea.

If the waiting is a couple of days that's completely fine to start exploring the idea. But if it's more like a couple of months there's a communication problem that needs to be solved.

As long as there's no conflict between these three persons, there's no reason why this should lead to authorship dispute. The key is to maintain clear and regular communication, and apparently the three persons involved are aware of that. A is right to seek their supervisor's advice, ultimately the supervisor decides who works on what. But in general there's absolutely no problem for A and B to work on the same idea and write papers together, as long as roles are clearly defined beforehand. In particular the question of who is first author for a particular paper should be clarified from the start. If relevant, the authors could target two distinct papers, one focusing on A's part and the other on B's part.

Note: this might depend on the domain, but I think most academics would agree that an idea by itself doesn't belong to anybody. What matters is the effort put into developing the idea into a proper scientific contribution, usually in the form of a paper: that's authorship. Of course, the person who had the idea should normally be the one developing it, but it's more a matter of common courtesy than of intellectual property.


Postdoc application asks for both cover letter and research statement, can they overlap?

Yes, you have it right. Just be very careful not to repeat yourself in either of the documents.

The reason they're asking is because they feel they are different enough documents that they should be completely separate, and you should probably treat them the same (in this case).


Finding good statistics for computer science matriculation (drop-out) rate

The National Center for Education Statistics in the United States surveys cohorts of first-time, beginning students at the end of their first year in post-secondary education, and then three and six years after first starting.

Per their official report, 59% of beginning bachelor's degree students in computer and information science in 2003-04 had either left post-secondary education without a degree (31%), or switched to a non-STEM field (28%) by 2009.

However, this number doesn't identify those who switch from computer science to a different STEM field as drop-outs. It also doesn't differentiate between

students who persisted in computer science and earned a bachelor's degree by 2009,
students who persisted in computer science but were still enrolled in 2009, or
students who persisted in computer science but earned an associate's degree or certificate by 2009.

Fortunately, the NCES also allows you to create custom tables from this dataset using the PowerStats tool on their website. (You have to create an account to use the tool.) This is a valuable tool if you're interested in exploring these statistics further.

Using PowerStats, I found out that among those who enrolled in a bachelor's degree program with a computer/information science major in 2003-04:

51.3% had earned a bachelor's degree by 2009
Of these students that earned a bachelor's degree by 2009, 67.6% said that their major when last enrolled was computer/information science.

So, 34.7% of beginning bachelor's degree students in computer and information science in 2003-04 earned a bachelor's degree in computer and information science by 2009 and 65.3% did not.

Here's part of the data table I generated for this answer:


What are some good practices for a supervisor?

As in any teaching situation, your job is to educate, not just watch over the student. This means, that you have some responsibility that the student continue to make progress toward their goals. You need to assure that they don't get stuck, or, rather, that they don't stay stuck for long.

This will take some time and interaction - regular meetings, reading their work, giving feedback, etc.

But, you don't have to give a direct answer to any particular question. What you need to do is to assure that the student has a way to find the answer, even if it doesn't come directly from you. Answer questions with other questions, for example, so that the student can have her/his own insights.

In the example, you give, it is better, IMO, to ask the student to tell you the tradeoffs of each method, A and B. You don't need to tell them to "go away and research it". Tell them to lay out the pros and cons of each method. If they miss something in their explanation, you can help them along, of course.

But if they have no idea of the tradeoffs, then you should probably send them off on a quest of learning.

The short form is "give them the minimum they need to keep moving generally forward". This lets them develop confidence over time, make the work their own, and, still, not get (or stay) stuck.

If done well, this will also put the student on the path to intellectual independence, which they will need as they continue.


Should all authors on a paper be comfortable explaining every aspect of the paper?

By most standards, authors of a scientific paper need to have made substantial intellectual contributions to the paper (e.g., coming up with the idea behind it, proving a required result, etc), made contributions to the write-up of the paper, and ultimately approve of the paper draft when it is submitted to a journal. As such, I think both you and your collaborator meet authorship criteria even though your grasp of topic Y is not as deep as your collaborator (and presumably your collaborator's grasp of topic X is not as deep as yours). At the very least, it is not dishonest to proceed as an author.

As for whether an author should be able to explain every aspect of a paper, I would think not necessarily. My field is very interdisciplinary, and it is not uncommon for clinicians to work with statisticians on papers. They are all experts in their respective fields, but their knowledge of the other person's field is almost guaranteed to be less than their collaborators. Yet, it is still possible for them to write papers together because their knowledge bases are complementary.


How should my name and affiliation appear in a scientific journal publication as a student?

In terms of “standard” conventions, I would suggest:

  Elizabeth G. Duncan, Department of Statistics, Virginia Polytechnic Institute and State University

If the research you’ll be publishing was conducted as part of a research group, however, you might list that affiliation instead, e.g., “Applied Statistics Lab, Virginia Polytechnic Institute and State University“


More than 2 months with status 'Editor assigned ' ; is it normal?

Contact editor and ask for status update.

Editor assigned generally means someone (whoever first received the submission) has chosen a member of the editorial board to handle the manuscript. It's because they haven't agreed to handle the manuscript that you don't have an assigned editor to email. It shouldn't take two months for the editorial board member to decide whether or not they can handle the manuscript, as well.

I would email the journal office or whoever you can contact and ask them what's going on. They might send a chaser to the invited editor, or they might invite a new editor; either way the ball's in their court.


Has a reference manager ever accidentally shared unpublished data?

This has happened deliberately, where an informal reviewer made the work of an author public without their authorization. One well-known example is Wallace's twenty-page abstract of what would become known as the theory of Natural Selection, which was mailed to Darwin on June 18, 1858 with a note asking it to be forwarded to Charles Lyell. Instead, Darwin, Lyell and Hooker decided to publish Wallace and Darwin simultaneously so that Darwin wouldn't lose credit for the work he had already put in (and would put into The Origin of Species and other books). This paper was read out to the Linnean Society of London on July 1, not leaving enough time for a letter to be sent back to Wallace in Malaya to check if this was okay. It's pretty clear that Wallace did not intend this manuscript to be published (as per Prof. Charles H. Smith):

  For his own part, Wallace later indicated in print on no fewer than four separate occasions that the manuscript he had sent to Darwin had not been intended as finished product: in an 1869 letter to the German biologist Adolf Bernhard Meyer (later reprinted in 1895 in Nature, Volume 52, on page 415), as a note added to the essay when it was reprinted in 1891 in Wallace's Natural Selection and Tropical Nature (on page 27), in the article 'The Dawn of a Great Discovery' in January 1903 (Black and White, Volume 25, on page 78), and in his autobiography My Life in 1905 (Volume 1, on page 363).


A statement such as this "© 2017 X"  means that the author want you to know that he is the author of this page, and that he has the copyright over the content of this page. In simple words, this means that this is some original content and that it belongs to him.

If you want to copy some of that content in your own webpage, book, or other documents, or modify it then you should do it in a way that will respect the copyright law  and the license of the content chosen by the author. If the author does not provide a specific license for his webpage such as Creative Commons, then you should ask the authors about how you can reuse his content and if he agrees or not. You can send an e-mail and ask him if you can modify the content and republish it for example. Maybe he will say yes, maybe no

But beside that, you can still cite his work. For example, if you want to copy a few sentences of text from his webpage, you could use the quotation marks " " and cite his webpage as the source of the text. In this case, you typically don't need to ask the permission for that because you are citing a short part of the text.

By the way, a book can be open-source (you can see the code of the book), but "open-source" does not mean that you are free to do whatever you want with the content. The copyright still belong to the author and you need to follow the license that he choses.


Considering that public telephone directories with names, addresses, and phone numbers have been around for decades, I don't think there's a significant risk of identity theft here. You could consider using a distinct email for your resume such that if you begin getting too much spam you could manage it separately, but even that's probably not necessary.


Can I still try to publish my work if my algorithm's results are not as good as other algorithms'?

If you want to get technical, in general no learning algorithm performs any better than any other.

The question then, is what can be learned from your algorithm.  In your question, you speak of it as a fond intellectual child that you wish to grow and nurture, and you speak of your personal concerns about acceptance and rejection.  Here is the thing, though: none of that matters for a publication.  What matters is this: what new knowledge or capability is brought into the world with your work on your algorithm, and how can this be objectively evaluated?

Here are some possibilities that I can see:

Your algorithm may perform better on an interesting and useful class of problems, and thus be of practical interest.
Your algorithm may perform worse, but have some other desirable property, such as executing very quickly or using very little memory, in which case the performance comparison just needs to show that it is sufficient, and you can show much better performance with regards to those other properties.
Your algorithm may perform worse, but do so in a way that is enlightening, e.g., taking a more human-like approach, or showing how something can be accomplished by a very unusual and unexpected route.  In this case, the performance comparison is simply showing that your algorithm does not perform too badly to be interesting, and the narrative should focus on the path taken to achieve your results and why that is interesting.
Your algorithm may only have taught you personally some interesting things about classification and scientific research, in which case you should mourn the passing of a fine research idea and move on with your life.

Only you and those who know your work well will be able to tell which category it truly fits into.


How to define author order of a collaborative paper where all authors have contributed equally?

Since your field does not normally do standard alphabetical ordering, then its use here might signify that something unusual is going on. So you could in principle list everybody in alphabetical order, identify the corresponding author, and then insert a note in the acknowledgments that everyone contributed more or less equally to the paper.

Alternatively, in some fields, papers can be authored by "teams" instead of individuals—although all the individuals participating in the team are cited somewhere. This is more typical when the collaborations run to the hundreds of authors rather than a few to a dozen. If the journal you submit to allows this, it would probably be the fairest option of all.


There is nothing wrong with citing paper, reviews, etc., which have appeared on the arxiv (and only on the arxiv). Go ahead and cite the paper.
(If your paper gets accepted at a journal, they might ask you to update in case the paper has been published in a journal in the meantime, but in the fields where the arxiv is commonly used, journals and referees will have no issues with references to the arxiv.)


This depends on the journal's style sheet, but usually you only list the references that are cited in the text. Thus, I would delete the superfluous ones (and renumber the notes).


My supervisor avoiding me -- what to do?

Professors are not always the people who would win a prize at interpersonal relationships.

Professors often have significant stressors in their lives.

So please don't assume this is about you.  For example, perhaps the professor will be up for tenure next year and is trying to crank out as much work as humanly possible, despite feeling almost crippling anxiety, and has decided that it's necessary to minimize non-productive interactions so as to maximize the hours in the day available for research.

If you yourself are feeling anxious, unsure whether you are cutting the mustard, then ask.  If it's difficult to ask this question in person, then you could send a preview of your question via email, a few days prior to your meeting, to give time to prepare.  Here is one way such a question could be broached:

  Dear Prof. X,
  I am enjoying working hard on my project!  But I would also like to find out how I am doing, objectively.  Could we check in briefly about this when we meet next week?  I am interested to know: What do you think is going well, what areas do you feel I need to improve in, do you have any suggestions for me, to get the most out of my time working with you, are there things you would rather I handle differently?  This is the sort of feedback I'm hoping to get when we meet.  I think that periodic constructive feedback will help me become an asset to your group.

Be prepared to take notes.  Don't argue or defend yourself.  Thank the professor for the feedback.  Don't get too frustrated if your professor doesn't know how to do this sort of feedback session smoothly.  Remember, the main purpose in asking this is so you won't have to rely entirely on your overactive imagination.


Should I address my GPA declination in my personal statement?

Triple-majored and still above 3.5? That's very commendable. Typically when you refer to declines in academic perfomance, it's because your GPA is STILL low, perhaps below the minimum requirement for graduate school. But you seem to have graduated with an overall great GPA, and you should focus your personal statement instead on what you've learnt and done, such as research, projects, jobs - instead of that one year where things didn't go well. I'm sure you have a lot to talk about as it is.

EDIT: While a good GPA is necessary, your skill set and recommendations from your superiors you worked with are also as important. You need to show the school you're applying to what you can bring your field, which is what a personal statement is there for in the first place.


What to wear for a PhD/ MSc thesis defense?

Almost anything will be fine, provided you feel comfortable on them. The clothes you are wearing will influence the first impression, but you are going to be talking about your project for at least 20 min, and the confidence and clarity will wipe whatever the first idea was. Make sure they are you feel good on them, and don't use them for the first time this day in case they itch or something (specially important for underwear!).

The right level of formalism is very dependent on the culture and setting, but it is probably not so important. It will also depend on whether the event is public or not: if the audience are going to be the people that have been seeing you in normal clothes all year round, or if the public is going to attend and the University wants to shine.
 Of course, a frock and a top hat or just a swimming suit will look ridiculous, but anywhere in the middle would work.

For reference,
I have been present to two PhD defences in Sweden (where they are quite lax in formalities). In one, the doctorand was wearing plain business-like clothes, slightly more formal than a normal day; in the other, he was wearing a normal shirt, quite less formal than his normal attire. And, for the record, both passed.

Edit:
Jigg is right in pointing that some universities do require a certain dress code. In this case, it will probably be clearly stated by the centre. Being rejected is possible, but extremely unlikely, as it can get the university in all sorts of legal troubles. Also, these regulations can get to absurd levels (the story seems to be a legend, but the third comment may be legit).


How to avoid "presentism" or "historical transposition" in writing papers?

Follow links on historiography - there are lots out there.  Historiography is both an academic discipline and a name for a text that outlines and contextualises a question with particular focus on how and why and when and where it was approached by whom.

Reading in this area will help you to understand why 'presentism' is an issue in academic writing and how to spot it in your own thinking and writing.

The other advice I can give is to say that if you pay attention to any good academic writing you will see that there are clear indications of what is intended as empirical and what is inferred.

Proper use of references and citations will help you to avoid accusations of being wholly subjective.  If you want to get across a value statement why not find a quote from someone contemporary to the event whose opinion mirrors your own.  Do not forget to include and consider opinions that contradict your own as well.  You can weigh the merits of an argument voiced by others.  Of course, ultimately, your findings will be influenced by your own background and social context.  Try to be clear and honest with yourself and your audience about when and how this is happening.


IQ and Probability of Success in Two Difficult Fields

IQ is a terrible test for anything but certain types of pattern matching and to aid in educational intervention, and its limitations are well understood by actual psychological practitioners.  There are correlations, but the correlations are pretty loose.  With all those caveats, according to Wikipedia, you are totally in a reasonable range to get a Ph.D..


How to give opinion to my professor about writing LoR?

I have two suggestions. The first is to give him an outline of what you think your accomplishments are and say something about your enthusiasm and future goals. Or, at least, offer to give him such an outline if it would help. This is just to give them a few ideas.

The second, probably more important, is that you ask another, more experienced, professor that is also writing for you, to speak with the advisor and also give them ideas about how to frame such a letter. It is normal for one professor to help out another, newer colleague, on their responsibilities.

I'll note that some letter writers actually ask the candidate for a first draft of the letter they will send. There is some controversy about this, but it is common enough that you shouldn't be surprised if it happens.


How to reference organizing conference symposia / panels on CV?

I recommend including a section at the end of your CV entitled "Service", where you list things like conference/panel organization, committee memberships, refereeing activities, and the like.  Initially you may have only one or two items, but the list will grow over time.  As this list grows, organize it into subsections (University service vs Professional service, for example) and subsubsections (editorial boards, program committees, workshop organization, proposal reviews, refereeing, ...).

(I'm assuming that you mean the American Academic CV, which includes everything, and not the UK Professional CV, which is just a two-page sketch.)


Am I allowed to share Stack Overflow data along with a paper that uses it?

The license information can be found at https://academia.stackexchange.com/help/licensing, which also has links to the terms of service.
That, in turn, has links to the API terms of service.


Is there a website for academic computer science jobs in the US like mathjobs.org?

The best source for CS jobs in the US is the Computing Research Association (CRA). They maintain a jobs site that AFAIK most departments post to.


How to survive as a postdoc with unsupportive mentor and team

I am actually in a situation that's similar to yours in a lot of respects (i.e. at the end of a postdoc and not that much to show for it due to lack of collaboration with my team for various reasons). So I'll give you some advice I have been trying to apply myself - although I haven't quite succeeded spectacularly so take it with a grain of salt.

It's a systemic problem. This is not practical advice on what to do, but emotionally, you need to try and kind of self-distance yourself from this situation to realize that academia does not encourage researchers - after their PhDs and before tenure - to go out on a lim exploring something deep that doesn't show immediate results. There are no mechanisms for consideration of effort and risk and potential impact of success, while an epsilon-improvement on the state of the art in what's fashionable is usually a sure-fire success.
Finding collaborators is job #1. Unless you can churn out award-winning work yourself, you absolutely must find collaborators. Maybe that means quitting the group, eventually. In the mean time, be very very active in contacting people who do work you feel you could build on or collaborate in, introducing yourself, talking about your plans etc. Possibly also out of academia if that's relevant.
Try to bargain with your mentor You're expecting your mentor to behave in certain ways, but s/he isn't doing so. You should have (and possibly still can) talk it out with him, in the sense of realizing why he is acting the way he is
If you can, try to get direct access to students You mentioned trying to work with tenured faculty's students. If you could somehow get in touch with prospective students yourself, that would be a bypass. Proposing to teach a workshop or proper course, or to co-teach something, or to offer a "lab project" course, or to give a guided tour of the lab's activities, could help. Of course, that has a cost in terms of effort.
Take the time/effort to also pick more low-hanging fruit Try to either branch out to a close/related subject, or work on a problem in your main subject of interest, which you think is not very significant - i.e. probably the opposite of your intuition regarding how to choose what to work on. While this would not yield a great publication, it could yield something publishable and opportunities to talk to people and make connections. It would also make it not appear like you're unable to produce anything in the bottom-line sense.
Explore collaborations with your PhD advisor and his/her group. You did well during your Ph.D; I assume the people around you did not all die in a car crash... talk to them, especially your old advisor if you're on good speaking terms. In fact, you could even ask for their advice on your predicament (that's orthogonal to suggesting collaboration).
Explore opportunities for funding. While this requires collaboration with a more well-established academic figure, you should still give it a try. In fact, it might be an opportunity to bypass your own mentor if s/he is not interested in helping, by talking to the more senior / most senior people in the lab. If you manage to secure funding, that would almost be like getting students; it would mean your lab and even your mentor would be more committed to promoting the research you're doing; and it's an important thing to have on your CV.

Note: These suggestions are not comprehensive and are not in any particular order.


Course on Moodle - how to download all student interactions?

For those with admin privileges in moodle they can access the log features to see anybody's activity in moodle. For a teacher this feature is available to see student activity at the course level only. The activity can be  viewed by student and or by the activity selected (forum, assignment, etc). The information provided isn't very deep. Just a time stamp with the student and what they did. However aggregating this info can provide some insights.


Google scholar citation and title issues

Answer to your first question: you want to import your second version (which Scholar considers as a different paper), and then merge it with the first one.

To import the second version, on your profile page click on the squared + in the line just above your list of publications, then the new title in the search bar should get you the paper.

Once imported, tick the first and second version, and click on "merge".


Convince coauthors of reducing self-citations

While you can give your best arguments to the others they probably won't be convincing. On the other hand, I wouldn't worry about it too much since the most powerful advocates for your position will be those who review the paper after submission. Reviewers don't especially like to go through "crufty" papers with a lot of irrelevant stuff. If your co-authors are, indeed, over-the-top on self-citation, it will likely be noted and need to be cleaned up after reviews come in.

Rather than cause too much difficulty, let the reviewers be your allies if it is really needed.

I would, however, make the argument to your collaborators that a lot of the citations are irrelevant and detract from the main ideas of the paper. You could even send them back a draft in which you have removed the citations you think are unneeded, just so you have a "working document" without those citations.


If you came to me and said upfront that you wanted to get research experience and wanted to work with a variety of professors rather than making a full commitment to only one, I would try to find a way to accommodate you.

Or at least I would let you know what my expectations are. But, in any case, we have an honest relationship.

Now there would be no question of an ethical bind if you later decide to work with a more prestigious professor.

But the honest relationship is very valuable given that the professors know one another and you don't want to get caught in a bind between two professors.


Can I submit a paper to two or more journals at the same time?

No, not the same paper in two journals at the same time.

Either submit to X again or submit to Y.


Searching for academic jobs within a specific city

If you intend to stay on the job market (whether for those 3 institutions or in general), the best thing you can do is stay competitive in terms of research productivity. That usually means taking a postdoc or other full-time research position where you can publish as much as possible.
However, there is a "shelf life" to postdocs. If you are a postdoc for too long, hiring committees start to wonder why you haven't been hired, and may reject you thinking there's something wrong. For instance, in my field it is common to have 0-2 years of postdoc, so someone who has been a postdoc for 5 years may find it more difficult to get interviews.


List *all* journals for which one has done peer-reviewing

I expect the answer depends on your circumstances.  Here are some cases that might apply.  I can't specify precise cut-offs between them, but I doubt it matters too much if you're near the dividing line.  (Keep in mind also that you may have specific rules to keep in mind.  For example, some particularly bureaucratic universities have guidelines for exactly what you must or must not include in your CV.)

For most junior academics, I think it's helpful to list all of them, and it's almost certainly not harmful, assuming they are at least respectable, mainstream academic journals, even if they aren't prestigious.  Each time you've been asked to referee a paper is a vote of confidence from an editor, and it's worth demonstrating that you are starting to become widely known.  Listing seven journals, some really not prestigious, probably looks better than listing just the two or three more prestigious ones.

For people coming up for tenure at research universities, and even more so for mid-career academics, I'd recommend focusing primarily on prestigious journals.  At this stage the goal isn't just to show that people have heard of you, but rather that editors of excellent journals trust your opinion about important papers.  (But be sure to add some short comment to make it clear that this is a selected list.)

Once you are sufficiently senior and widely known, I don't think there's any need to bother listing journals you've refereed for, except perhaps very briefly to indicate that you still do your duty.


Is it necessary for a grad student to respond to phone calls, as long as they're responsive on email?

Anybody who wants to participate in scientific life, even as a grad student, needs to have some way that they can be reliably reached in a timely fashion. They also need to provide that information to those who need to reach them (e.g., their professor, students if they are a TA).

Whether their recommended best means is by cell phone, by email, or by instant message, however, matters much less.  In fact, the current generation appears to be moving away from voice calls, so cell phone availability is less likely to matter in any case.

Thus, as long as it's easy for people who need to reach your friend to do so, the particular choice of not having a cell phone on should not be a problem.


Publishing master's research while in a different PhD program

It's fine.  Similar things will happen after the Ph.D., after job changes, etc.  Your current advisor doesn't need to be listed or involved in the process for work done elsewhere.
It is frequent (but unfortunate) that people write the thesis first and then produce articles.  However, I think it is better to be publishing along the way.  And this is not unusual at all either--so you are a little wrong that it is never done.  All that said, converting thesis chapters into papers is very normal and fine.
List the previous institution first with a footnote or parenthetical for current affiliation and contact email.  Do not list the old email.


There are a number of ways in which a DOI could be linked to a dataset:

Figshare will provide a DOI for any deposited work, which includes data.
Zenodo also provides DOIs for any kind of research output, including datasets
Dryad provides DOIs for data submissions linked to papers (for a fee, which includes storage, curation, archival, & checks for best-practice [HT @DaisieHuang for pointing out my lazy description of fee previously])

You might also look to see if a domain-specific repository provides a DOI for data. The journal Scientific Data maintains a good list of repositories you can look at.

Choosing a DOI provider will depend on particular circumstances. Both Figshare and Zenodo are both free to use services for example whereas Dryad charges for the service they offer to cover ongoing storage and archival costs.

Some points of comparison between Figshare, Dryad, and Zenodo, etc

Dryad accepts data relating to publications; if it isn't associated with a paper then they won't accept it. Figshare and Zenodo will accept any research output, whether linked to publication or not. In that sense Figshare and Zenodo are more broadly applicable to any research outputs.

Data may be more discoverable in Dryad or domain-specific repositories (DSRs) than in general purpose ones likes Figshare & Zenodo. Data is likely to be formatted in standard ways and more easily searched by online or other tools if they are archived in Dryad or DSRs. This is likely to encourage reuse.

Figshare is a for-profit commercial entity, Zenodo is run by CERN and was supported by the EU OpenAIRE project at one point, whilst Dryad is an not-for-profit entity supported by research grants and membership fees for organisations.


How exactly does a conference abstract differ from an article abstract?

To me an article abstract summarizes the entire article including the overarching questions through methods, results to the major conclusions.

A conference abstract will of course also summarize whatever is presented at the conference. The differences lie in several aspects of variable weight:

Conferences are often focused on a specific topic so one can be less stringent with the background
Conference presentations may involve work in progress and as such the final conclusions maybe quite hazy.
The conference abstract may be written before most of the work has actually been done (this is quite common with some conferences in my field) and becomes an "advertisement" for what might come.
The conference contribution may in some cases involve a paper but can also be a poster or an oral presentation. depending on which abstracts may contain varying levels of finalized conclusions.


Do I have to inform a graduate program that just admitted me about my attendance to a different program?

I can't see any need to notify the second program. It would be courteous, and may be necessary, to tell the current program, depending on circumstances. They may need to fill the slot you are leaving as is the case in many medical programs.


PhD thesis layouts from around the world

Use the one that is provided by your institution.  The formatting guidelines are not "guidelines", but are instead "requirements" that are checked by someone who deeply cares about them.  So you should use a template that has successfully been used in the past at your institution.  If you do otherwise, you are setting yourself up for a lot of formatting work.  All of that said, University of Oregon's style file, which I used for my degree there, may be found here: http://www.ctan.org/pkg/uothesis


What does a taught Master's admission board consider important?

So my question is: besides having strong letters of recommendation, what can I do to increase my chances?

Not much. You're applying right now, so there's no time to make your application look stronger.  However, in math at least, no prior research experience is expected for master's programs, or even most PhD programs in the US.  Your GPA looks fine to me.  I don't think you should have trouble getting into a good master's program in the US (in math or CS) provided you're coming from a quality school and have good letters.  You could also consider sending out some applications for PhD programs if that's what you want.


Unethical requests from the senior professors and chair

It sounds like there is such major lack of understanding regarding your job that you need to have a discussion with the Department Chair. You need to come away from this discussion understanding how and when your performance will be reviewed, what you need to do to either have your contract renewed or get tenure, and how you will be able to do that. Hopefully this conversation will resolve the issues, although from your description it does not sound like it will. More likely, you are going to need to meet with the Dean as you hand in your resignation. You should explain to the Dean that you did not fully understand the position when you took the job and that the expectations and behavior of the department are wildly inappropriate.


Is there any preference given based on how far in advance of the deadline a graduate application is submitted?

Look at all the application rules and guidelines. Unless the registration/application is specifically described as first-come first-served (which would be unusual), the date of submission doesn't matter as long as the submission is complete before the deadline.


1) You should start applying for jobs about 9 months before your current job ends.  Most employers will want you to start immediately, or within a few months, and might favor candidates who can do so.  Starting 9 months ahead is basically allowing time for the job search process, application processes, the interviewing processes, and employer decision-making processes.  All of those can take much longer than you'd expect (and much longer than is necessary).  You might be very efficient in your processes, but employers can be very slow in communicating with you, starting the interview process, and (worst of all) making hiring decision.

I say "about 9 months" because this is a very rough estimate.  You might do well to start a year ahead and you might succeed by starting 6 months ahead.  But don't start 3 or less months ahead.  There are many factors you can't control and you are not in a position to go many months without income.

If you get lucky and get an interview 9 months before you are available, someone might ask why you are interviewing "now".  Just tell them your job search plan and your priorities.  If they can't hold the position open for 8 months, then move on.

2) I'd say that your chances of getting a programming job are about zero if you have no previous experience or training in programming.  There are just too many other people who have it.

Your best chance is to apply for jobs that require PhD in Math and where you'd work in groups with programmers.  For example, you might find work in the field of cryptography as a mathematician and then get training and experience in programming along the way.  Same goes for jobs in Econo-physics (quant finance & trading).

If you have one year before you change jobs, I'd recommend taking one or two introductory programming courses -- Python and R are good choices.

You should also build social network relations with as many academic-to-industry mathematicians as you can, so you can learn who is hiring and how that maps back to your particular knowledge and skills.

3) I'm not familiar enough with (technical) publishing to know salaries.  I was recently a technical editor on a book, but that was a contract position and the pay was low for the hours I put in.


Is it possible to ask about RA positions after being rejected by the same lab for a PhD?

You can ask for employment, but the title and work would probably be different from that of an RA. And the opportunity for authorship of papers might not be available.
In some fields, labs are very large, usually grant funded. There may be more need for lab assistants than can be fulfilled by graduate students. Someone has to watch that the kettle doesn't boil and bubble too much over night.
Holding such a position could possibly lead to interactions that open additional possibilities. But you would be an ordinary employee, subject to rules and protections for employees.
For an extreme example, I doubt that everyone working on projects at CERN is a student or professor. On the other hand, some at least, of these people wind up on long long authorship lists when experiments succeed.


reference letter from current line manager?

It is common practice in UK universities. It would also be considered bad behaviour if your HoD was unwilling to provide a reference, or if he wrote a bad letter out of spite or revenge or similar. Of course, there are people who take it personally and are unpleasant when people leave so there's no guarantee he would be reasonable.

You should be prepared to have a discussion about why you want to change universities. Is it a promotion? Or is there a research group that is closer to your field? Presumably you applied for the job for some reason. You haven't said why you think he may not be happy. If you have been there only a short time, there might be some bad feeling. But people move all the time for all sorts of reasons.


The IT department bottlenecks progress. How should I handle this?

This is a partial solution I've used myself, and it assumes a few things:

You access your clusters remotely through a connection (like other answers pointed, cloud servers or remote), so where you work isn't exactly the bottleneck.
The software you use isn't OS dependent or has any special licenses
You do not have a ton of things hooked up from serial ports to measuring equipment and whatnot.

One thing I've done in this situation is, when you finally grab a ticket from IT, ask them to install a virtual machine like VirtualBox and have them enable virtualization in the BIOS. Most processors allow this nowadays. Make sure they install it properly or they will ghost again.

This basically allows you to install any Linux distribution you want (you need Licenses for Windows images), so it is an operating system where you have all admin rights. This completely removes the IT middleman if your case is just coding and clustering the data crunching since you don't need their permission to do things in the VM, and also shouldn't impact performance significantly.

If IT is worth half a dime, they will appreciate the solution, since:

It takes gargantuan effort to compromise the Host Machine through a VM if you are not malicious
Resulting lack of tickets from you needing something updated/installed.

Worst case scenario you can still alternate between both Operating Systems, and do small things in the VM with your admin rights.


How to write a cover letter to request a postdoc (not advertised)

First: make 100% sure there are no official calls for postdocs at their group. It will reflect badly on you, if you apply outside of a call, if there is an open call.

Then: Based on a (more general) guide on writing academic cover letters I read when applying for my postdoc, I would suggest the following:

Explain briefly why you are contacting them. Why do you want to work with them? Be kind but professional, point to the positive thoughts you surely must have about them, but don't try to flatter them.
Explain what you can contribute. Try to aim this towards something that is relevant for them, but do NOT tell them how they can use their skills - that's a conclusion they must reach themself.
Explain your future plans. Again, don't tell them how well those plans fit in with theirs. They might, but this is also up to them.

I would suggest to compress the cover letter more than one usually would. Most professors' inboxes are filled to the brim, and if you want them to read all your selling points, they must be concise. You can always attach a more detailed application letter with your CV, portfolio, etc.


When do you ask a professor if a visitor can sit in on class?

E-mail a few days in advance.

Just showing up puts everyone on the spot, and could end poorly. It could also turn your visitor off.


Pros and cons of supervising master's students as a postdoc

If you are planning a career in Academia that includes any non-trivial teaching component, it would probably do you good to get some experience with this. Whether it is enough to compensate for the time is a judgement call.

But, one thing that you need to learn as a teacher is that other people don't learn like you do. Every student is different and each has a unique way of learning. Things that are easy for you may not be for others. This is more pronounced at the undergraduate level, but even at the MS level you will get a sense of the kinds of struggles that students have by doing some supervision.

The experience may also give you some insight into coming up with the sort of problems that are appropriate for MS students. Problems that are hard enough so that something can be learned but not so hard as to require years of effort. Having a lot of problems at hand can serve your own research interests well.

A more remote advantage is that some of these students will continue to a doctorate. When they do, they will form part of your academic circle with you as a "senior" member. This can open possibilities for collaboration later.

I think there are a lot of pros for this and few cons as long as you don't take on too much initially. Since there is only one such offer currently, it might be worth it to dip your toe in that stream.


Obligation to quote source of grammatical knowledge

I would like to know if this is considered one of these goods, which cannot be owned and thus needs no quotation.

Academic citation isn't about ownership. It's not about copyright. It's not about intellectual property. It's about allowing the reader to know where you got your ideas. It's about recognizing other people for their work.

In many cases different people might describe the grammar of a language a bit differently. They might even describe different dialects of the same language. Different dialects of the language might treat the same prepositions as treating a different casus.

Maria Brenda wrote "The Cognitive Perspective on the Polysemy of the English Spatial Preposition Over" – a whole book over a single preposition and what it does in different cases.

If you cite a specific source for your list then a reader can understand of why your list looks the way it does. If the care they can go to the original source to understand how the list got created.


How do I deal with a stubborn co-author who won't respond to suggestions?

Rewriting the text doesn't necessarily qualify someone to be the first author of a publication. If you're using the intended first author's structural outline and just rewriting sentences, then I don't know if that's sufficient to usurp the intended first author's claim. If I were the PI, I don't think I would do that.

What I might do is place a note in the paper along the lines of "X and Y contributed substantially to the writing of this paper," where X is the intended first author and Y is the person who rewrote the paper.

Better still would be for the PI to work with the intended first author about the corrections that are needed, rather than just rewrite everything. Helping X to become a better writer will reduce the PI's workload in the long run.


Ignored Requests Open-Source Software from a Research Group

I think contacting the editor of the journal is your best bet. Contacting grant agencies will most likely not warrant a reply, and I don't imagine many of them have stipulations for sharing code (yet).

That said, I have been in a similar position numerous times, and I have had very little luck every obtaining the code. The editor will most likely not be willing to retract a paper because the author's won't share, and they have little incentive to do so, since it will at most garner a single citation, but could lead to more problems down the road (e.g., the code is buggy and you can't reproduce their results, etc.)

Another tip would be that senior people (i.e., PIs) usually have more luck at this kind of thing because they are harder to ignore and/or have contacts, but it can be harder to get the to actually do it, because it can become political.


Website for professorship positions in Germany?

I have covered this very recently in the answer to a related question.

Firstly, there is is Academics.com. It is a free service that should have you covered to a large extend. As a bonus, it is not strictly for offers in Germany, but also has some professorships in neighbouring countries (although coverage for those is rather spotty).

The most complete list is the newsletter sent out monthly by the "deutschen Hochschulverband", which is the union of German university teachers. This list is pretty much complete for Germany, but it does not have any info on professorships anywhere else. You need to be a member to receive this newsletter, and one can only become a member by having been employed in an academic post at a German university before. If you currently work in Germany (e.g, as a PhD student or postdoc), you are either already a member or can easily become one.


Am I allowed to process personal data on a cloud server?

To some extent, the answer depends on location. In the US, IRBs tend to be concerned with Protected Health Information (PHI). There are 18 things that are considered PHI and generally these can be easily stripped from research data. For fMRI and eye tracking data, you need to be a little concerned about two components of PHI

Biometric identifiers, including finger, retinal and voice prints
Full face photographic images and any comparable images

In the UK the term is Personal Data and the definition is:

Personal data means data which relate to a living individual who can be identified –
(a) from those data, or
(b) from those data and other information which is in the possession of, or is likely to come into the possession of, the data controller

Most people provide a data storage and archiving plan that outlines how they protect PHI/Personal Data in their IRB ethics application. Most IRBs that I am familiar with do not consider fMRI to be comparable to a full face photograph or allow the individual to be identified. This is despite fMRI researchers often being able to recognize each other's brains. Most eye tracking data that I am familiar with do not include high resolution images of the retina and would not be classified at PHI/Personal Data. People publish pictures of fMRI slices and eye tracking traces all the time. Prior to uploading data onto the cloud, you will want to confirm with your IRB what they consider PHI/Personal Data.


How do U.S. research institutions typically reimburse a faculty candidate's airfare costs for multi-city trips?

When looking for a postdoc and visiting multiple labs, I was asked to split the reimbursement for travel costs between the institutions. The exact details of how to split were left to me.

Most institutions expect to fund the entire trip for faculty candidates, so I don't foresee any problems with you asking them to pay less than what they expected.


I have the standard Kindle (the cheapest one) and it lets you highlight both pdfs and epubs.

However putting pdfs in your ebook can be quite annoying as the size of the page may not match the size of the ebook and it forces you to zoom and move constantly.

I've seen classmates being a bit more efficient than me (struggling with Kindle pdfs) with their iPads combined with both GoodNotes and Adonit Jot Pro.


Asking direct question about attitude in online survey

While you will get numbers with such a question they won't mean anything. This is the sort of question that people will naturally skew toward "positive attitude" regardless of their actual attitude. The second method will also get you potentially inconsistent results.

Instead, you need a set of questions that will be honestly answered, maybe responding to scenarios, and from which you can infer the attitude.

Asking "Are you smart?" gets just noise. Some people answer the opposite of what they truly are for a variety of psychological reasons.


Dissertation: How to properly reference earlier versions of working papers in the German academic system?

What I typically did in such a case was either a footnote at the title in the gist of

  A previous version of this paper appeared at XYZ Conference in 1201.

or a mention in the introduction with the citation

  This paper is based on our previous work [ABCD+ '01].

Two side notes:

If this is a paper and you submit double-blindly, you'd need to revise the statements accordingly. You might even want to remove them for review and/or inform the editor.
The information on previous versions and an explanation "what's new" belongs into the cover letter of a journal submission.


Why do law journals require a CV when submitting a paper?

I'm an occasional reviewer for a prestigious law journal in Canada. I mainly deal with articles that talk about data science in the law field.

Now, you're more likely to listen to my answer specifically because I stated my credentials. I gave you a reason to listen to me: I'm an authority on the subject. The main reason they ask for your CV is to give you an opportunity to do the same.

In my case, if the author doesn't have anything in his or her resume that approximates professional experience with data science, I'll pay closer attention. This is because, in my experience, the person is more likely to try to sweep his or her lack of understanding of a specificities under the rug. For example, he might talk about p-values and draw conclusions based on them, but then fail to mention the numerical values and/or the interpretation context (i.e. fail to define "highly correlated", etc.).

In my opinion, the CV is an intuitively valuable data point for the reviewer. Just remember that it's one piece of information out of several.

EDIT

I want to add that the CV alone does not and should not change the outcome. As a reviewer though, if you're talking about tech and I see that you have no relevant experience in it whatsoever, it helps me give you better feedback. A lot. I regularly take the time to give thorough explanations in my comments and the depth of my interventions will vary based on the CV. If you have experience in say statistics and you mess up p-values, I'll rip into you. It's that simple. Don't waste my time when you should know better. If you have no experience and make broad generalizations that turn out to be false, I will also rip into you, but I might be generous enough to offer general advice. If you have no experience and you make a slight mistake, then I'll be kind and helpful even if I don't accept your paper right away just because you're from Harvard. I'll provide links, book titles, articles, etc.


Should I be honest when someone ask which part of the paper is mine?

In perspective of contribution, there are only the three options already mentioned by you

the part in question is based only on work you did, or
the part in question is based on work others did, or
the part in question is based partially on work you contributed to.

In each case I would tell this frankly.  Seeing the publication as the whole thing, prior to submission, everybody who contributed substantially will read again the paper.  This is the then last (of hopefully many earlier) exchanges among the contributors to discus and to clarify why methods were applied this way, and not an other. So that everyone among the contributors sees intent and purpose of the publication, the way the "the journey is told", and the conclusions eventually drawn. (consent)

Some publications even include a little section, explicitly stating these contributions, in lines like "Jon Doe designed the experiment, Bob performed the experiment, Jane Doe performed the data analysis, Jon and Abigail P.I. equally contributed writing the paper." *) While I saw such in natural sciences with interdisciplinary work, I see no reason why such would not be possible in mathematics, too.

In an ideal world, should you happen to become the author of correspondence, you should either know every aspect of the paper, or (second best) easily know how to refer to the contributor in question.  This is indeed not a light responsibility supervisors / P.I.s have, especially taking into account the fluctuation of co-workers. (Keyword reproducible research).

*) See, as first example I come to fetch right now, page 16 of Hellinger et al. "The Flashlight Fish Anomalops katoptron Uses Bioluminescent Light to Detect Prey in the Dark" in PLOS one, http://dx.doi.org/10.1371/journal.pone.0170489, section "Author Contributions".


Applying for three PhD programs at the same school

This answer is coming very late, but may be useful to people who land up on this thread.

If all the three departments have faculty and research which are aligned with your research goals, there is no harm in applying to all 3 programs. The graduate committee is made of professors who are very well aware of the fact that almost all phd applicants apply to multiple phd programmes, the difference here is that they know where 2 other applications of yours went. They may ask you to set a priority, that's all. Showing interest is different from receiving an offer, professors may be interested in multiple candidates, but due to constraints give out offers to a smaller pool. They should not hold anything against you. If they do, you are better off not joining that programme.

I applied to 3 phd programmes in the same university, and got selected in my second choice. All 3 departments knew that I had applied to the other 2 as well. They had no issues with it.


How to remove the word "we" when discussing results in an academic paper?

I had the same struggles. The general solution would be to start using the passive.

It can be inferred ...
It is Apparent from Fig/Table ...
The results depicted in X would be always true ...

I actually dislike this style (since it is more boring; even though it is assumed the correct style to write academic reports, paper, thesis, dissertations etc. in Germany)


Marking a journal paper as “Minor revisions needed” for minor typos?

Unless you are reviewing for a truly lazy editor, it shouldn't matter.  No matter which selection you make, the editor will see from your report that you are asking for extremely minor revisions and act accordingly.

Generally, I recommend minor revisions in such a case, because authors might not be given the chance to correct typos in a straight acceptance, and they might appreciate a second chance to do what they should have before submitting (but almost no one does), which is to find more typos and correct them.  For every one that you found, they will probably find another one.


How does one remain focused while studying for the GRE?

A few things that helped me
Pomodoro Technique - Study for 25 minutes with a 5-minute break in-between.  After 4 Pomodoros, give yourself a longer break.
Timeboxing - Limit your study time to specific times of the day, like 9-4 with a lunch break.  This will train your brain to expect to focus during the time-window, then do other things after.  Combine this with the Pomodoro Technique to best utilize your time.
Retake a practice test at the end of each week - This will both get you as familiar with the test as possible, and let you take a snapshot of your progress.  This snapshot should happen during your timebox.  Arrange to take the test during this timebox as well.
Take at least 1 day off a week - Be sure to give yourself at least 1 day off a week where you do not study or do work.
See a therapist - Studying for the GRE and applying to grad schools is stressful.  It may help to deal with your ruminations so they won't be as distracting.  They may also be able to teach you how to manage stress and time better.
It sounds like you may have burned out studying in one week.  Take a day off.  Tomorrow regroup and try at least some of these suggestions.  You'll likely need to play with the times suggested, but they are a good place to start.
Finally, remember that a few hours of focused, uninterrupted time is better than a day filled with interruptions and poor planning.  Make sure you're getting quality study time, then look at increasing the quantity.