When data is required to be submitted, is it before publishing the paper or after paper is published?

Discuss the impending publication with your supervisor before submitting it for publication. A few reasons for this:

If your supervisor's name is going to be on the publication, you should absolutely talk to him/her about it, because publications should never be submitted unless they are approved by all authors.
If your supervisor cares about you, then he/she will want to know how you are progressing. Having a paper ready for publication is a notable milestone, so it is something to update your supervisor about.

If your data and models end up being used by other students, all the better for you, since it means they consider your work important enough to work on. They're not going to be able to publish before you since presumably your data and models are complicated enough that they won't be able to complete the work before your paper gets accepted, i.e. you have precedence.

The only scenario in which this could be a problem is if your supervisor is unethical enough to steal your results, give them to another student, and get them published in the new student's name ... but in that case, why is he/she still your supervisor? It would indicate it's well past time to change supervisors.


Did I anger my PI by not sending my data/notes after leaving their lab?

So first, it seems a little strange that after an entire year of work, they would suddenly be "too busy to take on undergrad students." Of course I am only speculating, but my guess is that they (rightly or wrongly) didn't think your project was going anywhere and decided to cut you loose. This would also explain why they didn't ask for your data or notes, and why they have since hired new undergraduates. If this is the case, this PI would probably not be a good choice when asking for letters of recommendation.

At any rate, to your questions:

  I'm not sure if maybe my project as a undergrad wasn't that important, or if I was unprofessional.

If they wanted your data or notes, they should have asked for them. I assume there was no directive that you failed to follow, such as "upload your results to the portal every week." So no, I don't think it was unprofessional.

Why didn't they ask for your data or notes? Two possible reasons:

In my experience, first-time undergraduate researchers do things literally hundreds of times slower than I can. So, I would likely start from scratch rather than trying to turn the student's product into something useable. Of course, this will vary by field -- I can imagine that some "wet labs" have very time-consuming processes for which undergraduate data would be valuable (if we trust the undergraduate).
Everyone always has more ideas than they have time. If an idea gets consigned to an undergraduate, it's probably not very high-priority. So, it could be that no one is pursuing that idea, or that a new undergraduate will start from scratch on it.

  Would it be late now, more than a year after I left, to send in data?

Personally, I would not offer. As noted above, this is unlikely to be useful; further, it raises the question of "if you thought I needed this, why didn't you provide it a year ago?"

  I was hoping to ask the PI for letters of rec for grad school but I haven't spoken with him for a while and I'm not sure if I left a bad impression when leaving the lab

I wouldn't worry about not having spoken with him in a while -- everyone is busy. And I wouldn't worry about the data/notes situation. But I would think carefully about the circumstances under which you left the lab -- generally, we don't fire students if we think they deserve a very strong recommendation. But of course there are exceptions. You can certainly ask "Would you be able to write a strong recommendation?"


The logos on your poster should indicate the author's affiliation.  Use the logo of the presenting author's university.

Never use the organizer, sponsor, or host logo unless you work for them.  People attending the conference already know what conference they are at.  This information is not needed on a poster.


Am I allowed to use personal conversation as a source?

I think it would be dangerous to source an unrecorded interview with a prominent person that involves opinion. Actually, it seems dangerous to do it if it is unrecorded and the rest of the first sentence just adds additional reasons.

If the person, at some point, objects to your characterization of their words you will have some troubles.

However, you can refer to personal communication in general if you have a record of it. One way to obtain the record is to send them a message (mail or email) in which you state your interpretation of their words and ask "(a) did I get it right, and (b) can I use that in a paper I'm writing?"

But a recorded and transcribed interview would also do the trick.

However, don't use things that could possibly be disputed without any agreed upon record, or without permission.


How to convince people of the time required to perform PhD research?

I often draw parallels to elite athletes since most people easily realize that athletes need to train and spend much time getting to where they are (and they usually also have some talent for their sport). The point is that to become good one has to spend lots of time and energy training. How easy it will be is unique to each person. Hence, it is also difficult to say how much time and effort each person needs to complete a PhD. Not that one has to be the best, but one has to be good enough to be at the top. Another aspect that I find useful in the parallel is that athletes usually love what they do, and it is an internal force that drives them. I sincerely believe that some such drive is necessary to complete a PhD without having to torment yourself too much.

When trying to explain the time perspective to prospective students the parallel might not be enough and it is usually difficult to make people realize the interest driven part. This is, in my case, due to the fact that people decide on trying to go for a Phd for many different reasons other than just a genuine interest in the subject. I will add that I do not mean such a drive is the only way through but it certainly helps.


How to further follow up after contacting project supervisor twice?

Too late to be useful, but I'm on an "unanswered questions" kick, so...

Yes, I would contact him again. The worst that can happen is that he is annoyed; the best that can happen is that you get your internship.

How to structure it? Concisely. Like this:

  Dear Professor, Sorry to pester you, but if we move ahead with this, I will need to get the signatures/stamps from my home institute this week. Is there any update about my status? I am still highly interested in this opportunity. Thank you, -Name.


Doing Ph.D in another country and Master in Italy at the same time, is it possible?

I'm not sure of the rules in those specific locations but it was my understanding that you can only be registered on a full time course at one university at a time. This is something you should check with both institutions.

Further to this, do you really think you would have the time to study for a Masters and a PhD at the same time and if you did do both then could you honestly say you were dedicating yourself 100% to one or the other? A PhD is not something to be done on a whim and requires a huge effort on the part of the student to complete.


Where can I expect to receive responses to applications for jobs in math departments at universities?

Based on my job search experience from a couple of years ago, there are three kinds of communications you might get by snail mail:

Equal-opportunity questionnaires, asking your race, gender, etc, for statistical purposes (usually not shared with the search committee).  Responding to these is optional, and certainly not time-critical.
Rejection letters.  Obviously these don't need any response at all, and they usually don't tell you anything you didn't already know; often they aren't sent until long after the search was obviously finished.
Formal offer letters. You'll know when these are coming, because you'll already have been informally offered the job by phone or email.  (And in some cases, you might have also had to negotiate what the offer letter will contain, though for postdocs it's more likely to be "this is our offer, take it or leave it".)  At that stage, you could ask the employer to be sure to send the letter to your home address.

All communications that are actually relevant to whether you get hired or not will take place by email, phone, Skype, or in-person interview.  Time is of the essence in hiring, and nobody wants the delay of snail mail for something that needs a quick response.


Any good way to tell a faculty candidate "We don't want you"?

Getting a rejection sucks. There is not much you can do about it. My wife and I have talked about this a lot and as candidates the only thing we wanted to know was how close we were and how we stacked up against the people who beat us. When sitting on search committess we have had various levels of success trying to inform candidates in the rejection letter about how many applicants, how many first round interviews, how many campus visits, how many offers, and was the position filled.

The other thing we do is make sure the letter starts off with we cannot offer you a position and then includes all the other information.


Writing a research statement in mathematics without having any research experience

Your research statement should set out the background to the problems that interest you, what you think you could contribute to their analysis/solution, and an overview of the approach(es) that you anticipate that you might have to take. People want to be reassured that you understand the nature of research (ie. how it differs to an undergraduate programme of work), that you have a substantial and interesting problem in mind, and that you are potentially equipped to make an original and nontrivial contribution to knowledge.


Firstly, you are certainly not alone in feeling like you are missing out on work. In the competitive world of academia, everyone feels this way at some point or another, though it is rarely because they are actually not doing enough work. Also, I can only imagine how difficult it must have been to start a PhD while working remotely, as you have no colleagues or peers around you to gauge the "normal" level of work. Once we are all allowed back to our offices, you will see that plenty of PhD time is spent not working at all... my office had regular badminton matches during the working day, or we'd all stop for a cup of tea together, or go out for lunch or to the pub as soon as the clock hit 5pm (or before) :).
You will honestly be more productive if you stop trying to force yourself to work solidly for eight hours a day. One of the great benefits of academic work is the flexibility: if you're having a terrible day, there's nothing to stop you working for a couple of hours and taking the rest of the day off; conversely, if you're having a great day, there's nothing to stop you working late, chasing the solution to your current problem.
Furthermore, you're a first year PhD student, meaning if you started in October you're about five months into your PhD, which is likely going to take you between three and a half and four years to complete. During an undergraduate degree, it's common to work intensively for short bursts, while completing coursework or preparing for exams. A PhD requires a completely different strategy.
It's often said that a PhD is a marathon, not a sprint. In my personal experience, this is very true. You have to learn to pace yourself, since you don't have external deadlines any more (possibly excluding things like submitting a paper to a journal, but that is likely a self-imposed and flexible deadline). The only one you have is your thesis submission, still more than three years away. You can't keep up the high intensity work for that long. As you correctly recognise, you will end up burned out.
My strongest piece of advice is to stop working at the weekend. Your brain needs a break to be able to think productively and creatively when you are at work. Try to prioritise other, non-mathematical activities during the evenings and weekends -- go for a walk or run, read a book, draw, practice a musical instrument -- what ever you can do to relax under the current restrictions.
If you are worried about losing momentum, try writing a short paragraph or list of bullet points every Friday afternoon before you stop work, detailing where you are and what the next step in your work should be. You can even do this at the end of every day, to help you get started the following morning.
Finally, do you have anyone close to you who you can talk to about this? I suggest mentioning it to your PhD supervisor, as they can probably help you with time management or prioritisation strategies (and if they're a good supervisor, I expect they'll reassure you that you are working hard enough, and can afford to relax). If you are not already in touch with the other PhD students in your department, then perhaps send them an email and organise an online meeting, perhaps a virtual pub session on a Friday afternoon, where you can all chat and relax together. You will soon learn that everyone has gripes and complaints about their work, and how busy they are etc. It can be good to let off steam in this way.
In summary: take breaks (as many as you think you need times two), stop working weekends (unless you really, really, really need to, and I mean "PhD thesis is due in a week and I just found a huge mistake in my analysis" need to), and try to talk to your PhD peers at least once a week if you can (and don't just talk about work!).


Re-submission of rejected manuscript without informing co-authors

You should apologize and admit you were wrong. Don't try to defend your actions. It is a head-slapping error. Send the apology to everyone. Offer to immediately withdraw the submission if anyone desires it. Ask for advice going forward. That should cover it.

All authors need to be on the same page for actions on their work.


How can I quickly and easily index my hand-written notes?

Disclaimer: I do not endorse any of the products in this answer, nor have I necessarily used them in the past.

I've circumvented this problem largely by switching to Microsoft OneNote on a Lenovo Thinkpad Yoga with a stylus. For me, it gives me the best of both worlds: highly-accurate handwritten notes on a digital platform. (I only wish it was an open-source solution!)

That said, if you aren't interested in using a stylus/electronic means of taking notes, here's a couple of suggestions:

Check out a product like the Livescribe Echo pen. Using their special paper, you can take paper notes, get a digital copy stored on the pen, and record the audio of the lecture (synced with the notes themselves). There's also the Evernote Moleskin notebooks, which are specially-designed for OCR.
Before (or after) each diagram, provide a little description of the diagram itself. That way, if you use OCR, you can search for the description instead of the diagram/equation itself.
Learn LaTeX (for the equations, at least). It's not perfect, but once you've got a good idea of how to write an equation in LaTeX, you'd be surprised as to how quickly you can type them in.
As you pointed out -- after scanning the notes in, annotate them yourself using an electronic PDF tool. Most of them let you add comments that can then be saved (and searched).


Transitioning from engineering to research as an undergraduate RA

You make it sound like engineering and research are two contradicting things, but I think this view is falling short. Of course there are shallow implementation and verification jobs, but there are also plenty of engineering jobs about R&D fiddling and finding clever designs and solutions, and then there are also (purely) academic jobs in engineering fields. Note that the boundaries between all of these are very much blurred and there is a variety of people in engineering ranging from hands-on tinkerers to purist mathematicians with completely different mindsets. Therefore, people in engineering hardly ever agree on whether some job or result is just derivative craft lacking conceptual contribution, useful high-level research, or disconnected theoretical work with pretentious notation but possibly useless and not much behind it. Also, implementation jobs can require a lot of clever thinking too, e.g. in analog electronics or large system integration.

Since you're at the undergraduate level still, I'd say it's totally normal to learn and follow preexisting ideas before engaging in great abstraction and developing your own branches. It's hard to make strong and novel conceptual contributions to your field if you don't know its basics. Do not underestimate the work put in by many, many very intelligent people before you (one tends to forget about this at times, e.g. when reading a bad introductory book) and rather try to gather their insights and grow from them.

About your problem at hand: I guess the best thing you could do, as far as that is possible in your environment, is trying to steer your next career choices in the direction of institutions and companies that value conceptual thinking and smart solutions and not only dull implementation workforce. Aim for courses, texts, project topics, internships, and contacts that push you more and more in this direction.


This varies quite a bit between universities and colleges within the US and probably even more when you consider the academic systems in other countries.

In some cases (particularly in smaller departments) the department chairmanship is a rotating assignment and whoever is currently the chair won't be the chair in a few years.  This means that they have to get along with all of the faculty in the department or risk retribution after they step down as chair.  In this system, although the chair is formally the head of the department the chair often has little authority over the budget (the department might not have an independent budget), hiring, and other important decisions.  The chair will typically consult with all of the senior faculty before taking any significant action.  I've served as a department chair in this system and I can assure you that it is totally unlike being a manager in industry.

At the other extreme, there are places where the department chair is a permanently appointed full time administrator with substantial control over budgets, hiring, and all important decisions.  These chairs have a lot more power, but even then senior faculty members may be largely independent of the chair's authority by virtue of their fame, grants, etc.


This is unlikely to be a formal term anywhere, but a person who does what professors normally do (research, teaching, ...) but without a formal position/job/salary, might well describe themself as a pseudo professor.
Without a formal relationship to a university, they are probably less bound by university regulations, except, perhaps in treatment of students, if any.
Charles Darwin, for example, might be described as a pseudo professor. He had the skills and did the research but wasn't formally related to a university (if I remember correctly).
Industry researchers probably wouldn't so self-describe unless they had some sort of volunteer relationship with a university. "Think of me like a professor, but I'm really not."


(How) should I describe the company within my bachelor's thesis?

or should I go into more detail like e.g. the history of the company?

No, in general, there's no need for that: your thesis is not a company's brochure. Provide enough information to present the context of your thesis, but don't add too much unnecessary details.

Anyway, I suggest you to discuss this also with your university supervisor: they surely know what is the policy or the tradition about this in the university, and they can act as buffer between possible company's requests and university requirements.


Do prestigious mathematics journals discriminate against young (undergraduate) authors?

In fact, I published a paper in the Journal of Algebra based on work I did as an undergraduate (I was a graduate student by the time it was published).

Certainly, there's no policy discriminating against undergrads (or anyone for that manner).  It's hard to rule out very subtle ways that cues affect people's judgement; it's actually quite rare that I am asked to referee a paper by someone I've never heard of, so I do notice and probably adopt a more skeptical attitude when asked to referee a paper by someone whose work I have no experience with. Still, this is a subtle effect, and there's nothing to be done about but to do good work and get your name out there.

Actually, there's a decent chance that the editors and referee won't notice that you are an undergrad.  (If they do notice, it will likely because you are affiliated with a university where they expect to know any professor in your field, and thus will investigate when they see an unfamiliar name.)


Is there any way to post my code on Code Review Stack Exchange and not be worried about plagiarism?

In addition to all the good answers you received so far, I should also point out that in general people's fear of being unethically scooped is vastly exaggerated. I would imagine that there really isn't a community of people scouring the Web for master's thesis level research that they can find and then, with considerable time disadvantage to the original author, copy. I say "with considerable time disadvantage" because even if somebody finds your work, they still need to reverse engineer a lot of what you already have and know to get to a publishable thesis or paper from your code alone. Unless you consider letting your work sit for half a year it seems unlikely that a copycat will end up publishing quicker than you, the original author.

Yes, being scooped sucks, but it usually does not happen because somebody stole your code, or even your idea. Scooping happens because there are multiple independent teams working worldwide on almost any mainstream research topic, and there usually only are a finite number of ways to attack any given problem given the current state of literature. Situations where two teams are working with similar approaches on similar problems are bound to come up.


When receiving an answer to a question do you respond with thank you?

In terms of etiquette, yes. A simple "Thank you sir/mam" helps acknowledge their response. The alternative is to say the thank you to them when you meet them the next day.

Reason: Unacknowledged conversations tend to leave a doubt in anybody's mind about whether the response was useful to the recipient or not. Certain people tend not to reply to an email if they were offended or if an email didn't help them. So in the same way we were taught it is good manners to say "thank you", it helps to do the same via an email.


How to list my name in publications, given that I am referred to by my middle name?

You can write your name however you prefer, so long as it is clear and consistent.

A good example of a person with your same situation, however, is Chris Anderson at Berkeley, whose publications list:

  J. Christopher Anderson

As you can see, he has come to the exact same solution that you suggest.


Can I change the referee once the letter of reference has been submitted?

The importance of letters of reference is covered in many other questions on this forum, and I won't discuss it here.
As for changing letters of reference: Most systems are set up to just take as many letters as are submitted. They will then all become visible to the selection committee. In other words, there is probably little you can do about the already submitted letter short of writing to the selection committee to disregard that one letter -- but that raises so many other questions that I don't see that as a winning strategy either.


Dealing with a huge block of similar definitions between two papers

Just tell up front that the terminology/notation used comes from the source you used (probably they do have a book or summarizing paper which explains it clearly). Nothing wrong with that.


Degree programs or careers with a focus on plagiarism detection?

Dr. Stefan Weber (PhD in Communication Sciences from University of Vienna) has essentially made a career out of detecting plagiarism, mainly in doctoral and habilitation theses from important public persons in the german-speaking area. You can find some information about him online. He has written multiple well-selling books on the topic, sells plagiarism checks, and regularly appears in public discussions.

However, note that the life of somebody who frequently and very publicly raises strong allegations against professors, politicians, and other degree-holders with substantial influence is not necessarily a fun one. As you can imagine, a lot of dirt gets unearthed and thrown in his face routinely (sometimes justified, sometimes more as part of counter-campaigning by the persons he attacked).

In summary, I think he fills an important societal niche in our area, but I really wouldn't want his career.


Is it moral to contact a questionnaire participant because of alarming response?

I know I've read something in a research textbook about unexpected ethics problems, but I don't remember where or what it said.

I think you need to contact your ethics committee (or equivalent), preferably quickly, for guidance. If there were enough questions about welfare on the questionnaire to be likely to bring up some sort of similar response, you should probably think about pre-empting it next time and automatically including links to suitable resources. It may be that now you can send out details to all participants (those who left email addresses, or perhaps the original distribution list, depending on how participants were recruited), as a way of offering help without singling them out. If the wording of the email address field requires it (I can't quite make sense of it), you could perhaps do so together with the results of the research, or a preliminary summary of the results...


I disagree slightly with SolarMike's answer. The academic hierarchy in the UK is very informal. It is fine to use first names for everyone, be they professor, admin staff or cleaner. A simple "Hi Bob" is fine in emails or in person.

I would argue that it would actually be a bit strange to address someone by their title and last name. If you did so, I expect they would quickly tell you it's fine to address them by first name.


Is it valuable to present a paper at an international conference?

I've got a fairly pessimistic view of the value of publishing in obscure, questionable places.  As an admissions committee member, I periodically see applicants with papers in journals or conferences I've never heard of.  Without more information, publishing in an unknown venue is completely meaningless, since the world is full of junk venues that will publish literally anything.  Many of them claim to do peer review and enforce scholarly standards, but they will actually accept nonsense text.  Unfortunately, there are no magic words (like "peer review" or "international") that will certify a publishing venue, because some venues simply lie, while others are honest but incompetent.

When I run across a completely unfamiliar venue listed in a graduate school application, I do some quick web searches to try to find out more about it.  Sometime I discover that I should have known about it, or that it's a perfectly reasonable and respectable venue that just doesn't have much of an international reputation, but often it looks pretty suspicious to me.  In those cases, I have one of two reactions, depending on how the application comes across.  Either I think "Oh no, this applicant was tricked into publishing a possibly worthwhile paper in a worthless journal", or I think "Hey, this applicant is publishing in a worthless journal to try to manipulate the system".  The former is more likely, with the latter being mainly when the application contains unseemly self-promotion or exaggerations.  Being tricked is mildly negative, since it suggests the applicant was naive and insufficiently careful, but it's not such a terrible thing.  (The main outcome would be that the paper counts for little or nothing.)  Being manipulative is very bad.

If you can't evaluate a conference yourself, it's important to seek advice from people who can, since sending good work to a bad venue is not a winning strategy.  As for MISG-2015, I can't speak from any direct knowledge, but the list of topics strikes me as absurdly broad, and I find it difficult to believe any scientific committee of twelve people could possibly do a responsible job of handling submissions from such diverse areas.


Should I inform about an updated CV post deadline? (CS PhD USA)

Should I send the places I applied an e-mail saying that the paper which was in review (and mentioned in my SOP/LOR/CV) got accepted?

No. Your CV/application is a snapshot in time, institutes likely won't update your CV/application, and they don't need such an additional burden. (Especially after two months, institutes are likely nearing or have made decisions.)

Does it have any effect on their decision?

It would improve your CV/application, equally it may annoy the institutes: It may have a positive or negative impact.


Is there any website for postdoc jobs in Canada?

I am one of the editors of https://www.thePostdoctoral.com - We had keywords "mathematical modelling biology" - last time May 2018 (https://promiseagep.com/2018/04/30/post-doctoral-research-associate-mathematical-biology/). There were 3 more in April and January.

Up to 250 new postdoc positions every day. We search the web AND social media and cover almost all webpages. Once they post or announce it's in our data base, before being shown in search engines.

If you want to have access to our data base simply sign up. Our power function is an archive keyword search (up 365 days, makes sense for 30 days or so).

Hope this helps.

Good luck and all the best,
Anthony from thePostdoctoral.com (and https://nextPhD.com and https://PhDvibe.com)


Why are dates (of writing or publication) missing in scientific papers?

Scientific papers are usually published in journals and conference proceedings. Publishers report at least the publication year and month, but may also report more information, like the submission date, the revision date and the date of the first online publication.

Your example is just a preprint, not the publisher's version, and does not contain any information. However, you can find the published paper at this link, where you can freely download the pdf with the publication year. You can also read the front matter of the proceedings to find further information.


How to cite the US Federal Register in Harvard referencing style?

My approach would be to give an in-text citation as:

Federal Register (2012)

The end-of-paper reference could be given in one of two ways:

Federal Register (2012) National Forest System Land Management Planning. Federal Register Vol.77 No.68, 21161-21276. Washington D.C.

or....you could cite the online pdf version as follows:

Federal Register (2012) National Forest System Land Management Planning, Federal Register Vol.77 No.68, 21161-21276 [pdf] Washington D.C.: Forest Service. Available at: https://www.gpo.gov/fdsys/pkg/FR-2012-04-09/pdf/2012-7502.pdf [Accessed 27 June 2018].

I think it's important to remember that the purpose of a citation is to help the reader to be able to access the document in question.  In my examples above, even if there may be potential disagreement over authorship (is it the Federal Register, US Govt. or Forest Service?) or location of publication, the reader can easily find the document you are referring to (especially the second option, which takes them directly to the online pdf).


Step 1: Gather data. For an appropriate period of time, keep a record of who asks for what task and how long each task takes to do. If you have comparable control data from before the requests started flooding in, track progress on your own project also, so that you can demonstrate the damage to your own work.

Step 2: Bring the problem to your advisor. Show your advisor the data. Explain what you need in terms of time: X amount of time for your own work per Y work period. Ask your advisor how best to make that happen (do bring ideas if you have them, but be open to things you haven't thought of).

Step 3: With your advisor's support, bring the problem to the rest of the research group. You should do this with proposed solution(s) in hand (one common Organization Hack is to bring two or three possible solutions, any of which would content you, in order to limit the apparent options to wins for you).

Derailment is possible here, especially if your advisor is unsympathetic, but a calm and data-driven approach is likeliest to achieve your aim.


Can we see the reviewers decision in the rebuttal phase?

In general, the program chairs want to know early which papers should be rejected directly without a rebuttal. To this end, the reviewers provide preliminary decisions with their review. These preliminary decisions are often changed later, based on the additional clarifications from the rebuttal.

The preliminary decisions are usually not visible for the authors, but this can vary across specific conferences.


Responsing to "How do you intend to fund your studies for the entire duration of your stay in ...?"

Maybe I'm missing something. But if this is a US Ph.D program, this question is really "Do you want us to fund you" and the answer is always yes. As JeffE says, you should not consider entering a Ph.D program unless you're being funded. Apart from the financial constraints this puts on you, the funding creates a commitment (by the department or advisor) to look after you. If the funding is from a research project, then you're even more sure that your work will be linked to something fruitful.

While there are many caveats to what I just said (and they're ringing in my head right now), they're not relevant at the time of applying to grad school.

So please always answer "I expect you to fund me".


Could research data fall under the Freedom of Information Act?

The original Freedom of Information Act applied only to information in the possession of government agencies. That means that the release of reports and proposals submitted to the funding agency could be compelled under the FOIA. But it did not apply to data from the research, if in possession of the PI and not the funding agency (as is typically the case).

A later amendment (Shelby amendment) expanded the FOIA to apply to some federally funded research data in the possession of a non-profit institution, as follows:

The release of "research data relating to published research findings produced under an award that were used by the Federal Government in developing an agency action that has the force and effect of law" may be compelled under the FOIA, if
the data is not "trade secrets, commercial information, materials
necessary to be held confidential by a researcher until they are published, or similar information which is protected under law."

Also, the requestor may be charged a "reasonable fee equaling the full
incremental cost of the agency, the recipient, and applicable subrecipients."

So the general answer to your question is that in most cases, the FOIA does not compel the release of data from federally funded research.

Regarding state law, it seems from the appendix to this report mentioned in another answer that at least one state does have an open records statute that may apply to research data produced by employees of the state university system:

  "Measuring Reproducibility in Computer Systems Research." Christian Collberg, Todd Proebsting, Gina Moraila, Akash Shankaran, Zuoming Shi, Alex M Warren. March 21, 2014.


For a postdoctoral/Ph.D. position in Mathematics in Europe, can I make this somewhat irregular request?

In several European countries, for example Germany, Switzerland, or Austria, it will be possible to fill positions in part-time. Whether you then actually work only part-time or not is a different question. In these countries, there is in most cases not a big difference between PhD students and post-docs regarding organizational details of employment, or even salary on a full-time position.

So the way I see your plan possibly working is as follows: A professor has funding to employ someone full-time for 2 years. You could then try to argue that in addition to working on the particular project, you also need time to educate yourself further and get only a half-time position, but stretch that to 4 years. You may want to communicate that it still means that you are working or studying full-time on project-related topics. If the funding is flexible regarding the year when it is spent (which is sometimes, but not always, the case), then I'd guess you have good chances that people are willing to make that deal.

This plan is probably best discussed with the professor offering the position, informally before you apply for the position, or when you go for an interview.


What happens to the reviews that people write for journal articles after they're sent back to the author?

In my experience, the contents of the comments of other referee reports are only made indirectly available. Since the authors are normally expected to provide a response to the reviews, the relevant criticisms and comments of the other referees are typically mentioned or discussed in that document. Outside of that, however, there's often little direct sharing of referee reports. None of the eight or nine journals for which I've reviewed (physics, chemistry, chemical engineering) have allowed me to see directly the reviews submitted by the other referees.

At any rate, the results are almost always kept confidential, unless it is an "open" referee process by design. (There are a few journals now that make the refereeing process a part of the publication record for a given paper; an example is The Cryosphere.)


What should an unofficial transcript consist of?

Yes, that's probably fine.  The list of courses, grades and GPA is about all that an official transcript contains anyway.

You can include a note to the professor asking them to contact you if they need anything else.


How to keep up with new publications and conferences. RSS feed?

Yes, the sea of information is immense, but you can keep a pretty good handle on it, especially with the tools available today. And one key to remember is that research is done by people. Often there is a core group of scholars in each field that do the most to move that field forward. Here are a few ideas of what you could do, and certainly there are more:

Use alerts on Google Scholar or other search engines
Follow other researchers in your field on social media
Meet some of the other researchers in your field, if you haven't already, and keep in touch with them
Do a search every so often just to see what is out there. You can also search in other ways, such as for a particular researcher or group and see the direction their articles is going in.


What is the scientific term for a “research gap”?

"Literature review" would be a good term. It refers to the section in a paper where you review the existing literature and show where your new piece of research fits in.

Don't confuse this with a "review article", which summarizes and integrates a large number of previous publications, typically far more publications than you'd review for an original article. A review article typically only does the synthesis, and does not add any original research of its own, although it may well point out gaps in existing research for subsequent investigations.

In you want to draw specific attention to the fact that the question you will investigate has not been covered in previous research, you could call it "open questions".


How to reply to an academic interview invitation?

If they call you and you answer, be excited and happy and keep the conversation really short. The person who called you does not really want to talk to you, they just want to tell you that you got an interview and possibly to dump some information on you. Your side of the conversation could be:

  This is so great and I am really excited to come for the interview. I have to run to a meeting/teach (doesn't matter if it is true or not) can we set up a time to talk in more detail later today or tomorrow?

At that point the person calling will either setup a time or tell you they will email you the information they need to tell you.

If they leave a voice mail, you can either call them back or send them an email, unless they tell you to do one or the other. If they email you, you should probably only reply with an email, unless they tell you to call.

In the follow up conversation/email there are things you need to know, which search committees often forget about. You should of course express how excited you are to come visit and tell them about your work and learn more about them and their cool work, but you do not need to directly sell yourself at this point (or really during the interview itself). What you do need to do is:

Setup a date for the visit. You should tell them when you are available.
Alert them to anyone you want to meet during your visit.
Find out how travel is paid for and arranged.
What the interview consists of and who will be at those events.
If they need a title and/or abstract, and if so when, for the job talk.

The reason you need to know what the interview consists of is that a campus visit may include one-on-one meetings/interviews, a panel interview, a research seminar on your past work, a teaching demo, and a "chalk" talk on your future work. If they want you to teach an hour lecture of an actual calculus 101 class, you really need to know that beforehand. Alternatively, they might want you to talk through a syllabus of a graduate class you would teach. A 10 minute research talk aimed at the search committee is very different than an hour long seminar with undergraduates present.


Do most professors in North America eventually have to give up directly doing research for a purely managerial role in research?

Only give up research if you can't do anything your students can't. Until then, if you continue to do research, you'll do things your students can't.


Would a graduate program require a transcript from a past institution even if the transcript is empty?

There are two issues at play here:

You received (or had opportunity to receive) goods or services at a cost and now you do not feel you should pay for said services.
You have asked if a graduate program would require a transcript from a school you attended but received no grades from.

My answer to these questions would be as follows:

If you did not withdraw from the university before the withdraw deadline, you indeed owe them tuition. This is how tuition works. You receive services from the university and you pay them for said services. Failure to attend class does not remit one's tuition obligations. That is the precedent. In essence, laborers came to your house and painted your living room. Originally you had agreed for them to paint your entire house, but you decided you no longer wanted the whole house painted. Do you still owe the painting company money for painting your living room? (Answer: Yes).

There may be several paths you can take in regards to the tuition charges. You can set up a payment plan with the university. This will allow you to pay back the tuition over time while also avoiding your credit being destroyed by your account being sent to a collections agency. Another approach you could attempt is to speak with the university and seek to have your tuition charges dropped because you could not attend class. Be prepared to prove that claim (if true). This would be a path you could take if you were hospitalized for the extent of the semester and you were incapacitated to a degree that rendered you unable to take the appropriate administrative actions and withdraw earlier. The university is extremely unlikely to remit tuition charged to a student who had claimed, yet unprovable, difficulties in attending class.
As for whether you need to provide transcripts for a university you never received any grades at, I would guess that it is rather unlikely that an admissions committee would require your transcripts if you sought prior direction from them on the matter. Simply email the graduate coordinator and say

  "I attended the University of ABC123 during September 2018. Due to health issues, I withdrew from all of my classes before final grades were issued. As such, any transcript from U of ABC123 will be effectively blank and will not contain any grades. Will the admissions committee still be looking for this transcript?"

If I received an email like this from a student I would probably reply and tell him or her that we would place a note in his/her file mentioning the situation and that they should not worry about sending a transcript. (Although, if I knew that the student owed another university $1500 of tuition, he could send us whatever he wanted and I would probably still reject his application. There would be no way that I would go dancing with that type of baggage).


How would someone go about creating something like the Pew Research Center?

If you wanted to create something like the Pew Research Center, you could just take a look at their history (that's their own, or you could check Wikipedia) and see how it was done in the first place (founded in 1990). The short version: a newspaper company wanted survey data to be able to report on, and so they created a center to do just that. It was then spun off into a charitable trust supported by various and sundry donation sources.

So if you wanted to take a lesson from their founding director, check out Andrew Kohut's history according to Pew or according to Wikipedia. Note that the Pew Research Center was a late-career project for him, and he served many smaller positions inbetween.

You could similarly check out the history of the Gallup organization (founded 1935), though a more recent example might be The Gapminder Foundation, founded by the late great Hans Rosling (he talks about his own personal life-long journey in this last book, Factfulness - a great book, IMHO).

In general, most organizations with this sort of large impact were founded by a combination of people with a business/financial interest (charitable or otherwise), as well as people with an expertise often driven by years of working directly in the field. Kohut did it serving years for survey/polling companies and had a graduate degree in sociology, Rosling did it after many years serving as a medical doctor and specialist in public health, etc.

A research-focused graduate degree would probably be hard to do without if you wanted to be a subject-matter specialist, while a graduate degree focused on professional preparation around business/fundraising/etc. would tend  to be most helpful if you are not already independently wealthy and highly connected and wanted to be involved on that side of it.

Another path, rather than starting from scratch, is to seek out organizations that are already operating in your country with a similar mission, or to look for organizations operating in other countries that already have or might be interested in expanding their operations to another country. Find what sort of positions they have, and then look to see what requirements they look for, so you could obtain direct experience without needing to start from scratch. If you wanted to start their own, chances are you would be competing with them directly or indirectly anyway, in terms of funding, public attention, etc. You should be able to find potential opportunities for volunteering, internships, etc., where you could be involved before you've finished your education, which would help you ensure this is what you want to do and give you a big leg up in getting started.


Letter of recommendation from REU professor

It is extremely valuable to have letters that speak to multiple sides of you as a student, e.g. as a scientist, as an academic, as a communicator; letters that say you're not one-dimensional. If you have no one else who can speak to you as a researcher, I'd absolutely recommend asking your REU prof to write you a letter. Further, if you have truly made a connection, or they really think highly of you, or anything like that, they could trump a letter from your institution, to be honest. Internship advisors' letters from places like NASA centers were key points in some of my peers' applications in the past; 10 weeks is a good amount of time to show someone what you can do, although a longer relationship (stay in touch, etc.) certainly helps them understand your depths.

I'm not sure as to how much any particular program might value a diversity in your letters, but your professors at your school benefit from having their students do well; your REU advisors benefit too, but on fewer levels, which may make a letter from an out-of-school research advisor weigh a little more heavily. Your mileage may vary on the last, though.


What is an "Advanced Studies Diploma" equivalent to?

As a PhD student from the Universidade de Lisboa (https://fenix.tecnico.ulisboa.pt/cursos/deic/curriculo), who is also a student of mobility (Erasmus Mundus), I hope I can add some of my observations which might be helpful.

Advanced Studies Diploma is everything of PhD, except the PhD defence (since it also includes the research proposal defence, that we call "CAT"). In my university (IST-ULisboa), CAT usually comes by the end of the 2nd year. To pass that, you would already have a solid research plan with possibly a few publications and research done.

So, this is part of the PhD (in IST, "Advanced Study Diploma" is used interchangeably with PhD), than a prerequisite to be accepted to a PhD.

I would assume, you already have completed your masters and half-way through your PhD since you have completed all the course works and defended the research proposal, hence making you a "PhD candidate".

However, unless you already have some arrangement with another university or a professor in another country (as in Erasmus Mundus and other exchange/mobility programs), I would strongly advice you against contemplating the idea of migrating/halting half-way through. It is not going to be easy to move your credits to the new university.

With your advanced courses, you may have gained some expertise in academia and research. However, it will be still something half-done than a complete degree. But this part is just my personal opinion. You may list it as an on-going PhD in any case, I suppose.


How to tell someone, that someone else "can"not answer a question I asked multiple times?

This is somewhat of a frame challenge, but I suggest you try asking the question on Physics.SE (or Math.SE, or even MathOverflow, depending on where it fits best) so that you can become the person who can answer the question.


Listing presentations at a conference side-meeting on a CV?

Yes, I don't see why you couldn't include this, as long as it's clearly understood that you didn't present a peer-reviewed paper at that conference.


Should PhD students mention small grants on their CV?

Just to be clear, it depends on what you are calling grants.  If you apply to an (internal or external) program that has some sort of name (e.g., University Student Travel Grant), then yes, this counts as something you can put under the "Awards" section of your CV.  (Incidentally, related question: List dollar amount of small grants on C.V.?)

If, however, you mean you got money from your advisor's grant, or the conference had a grant that provided you travel money (even if you had to request it), or the university automatically funds you, that does not count as an award.


Should I reject a specific historic fact and not include it in my work? Advice needed on reliability of source

It’s useful to consider the potential harm in making a wrong decision of either kind here. If you don’t mention the historical anecdote in your paper but it’s actually true, readers won’t miss out on much, and in any case won’t be actively misled — after all, you’re not claiming the anecdote never happened, you’re just not mentioning it at all. Those readers who want to learn about Boris Belousov’s life can still go and look for additional credible information about him. Presumably they will run into this anecdote. And your paper is in any case a science paper and not a history paper, so no one can accuse you of depriving anyone of critical information.

By contrast, if you mention the anecdote but it’s not historically substantiated, you do a great harm to your readers and to Belousov himself by helping to perpetuate a fallacious myth about him. The harm caused by this type of mistake is much greater in my opinion.

Another thing to consider is the credibility of the source and the level of scholarship that backs up the paper’s contents. The author of the paper you linked appears to be a high school student, and the journal it’s published in is a journal with low standards whose specific mission is to publish the work of budding researchers who don’t yet have a bachelor’s degree. The author doesn’t give a specific reference for the source of this anecdote, making it unverifiable. That’s not good practice, and it may reflect poorly on you to cite such a source without warning your readers about its potential lack of credibility if you rely on it for any information you were not able to verify from other sources.


How strict are paper revision deadlines?

The strictness of the deadline strongly depends on the journal and the context of publication.  For most papers to most journals, there is potentially a great deal of flexibility (assuming that you ask early and are polite about it).  The main exceptions that I have encountered are:

High-impact journals sometimes expect you to drop everything else on their behalf, and thus may give both a short deadline and little flexibility.
Articles submitted for a special issue sometimes need to hit particular dates in a production schedule, and thus may not have much flexibility to give.


Does giving compliments to the fellowship help?

Leave it out.  I think it definitely comes across as fawning.  It's clearly irrelevant to your qualifications and plans, which is what the personal statement is supposed to be about, so it shouldn't be included.

If the fellowship's administrative staff have been particularly helpful, you could send a separate email or letter saying thanks.  But this shouldn't be part of the application.


Is there a way to improve my grade after graduation?

There's nothing you can do to change your grade on a completed degree.  What you can do is do well in your job so that no one cares about your old grades, which it sounds like you've done.  So congrats on that!  The real issue here isn't your grades, it's that you're still feeling a lot of anxiety about your college experience.  I'd suggest talking to a therapist about that.  You can't change your grade, but you can better understand the feelings you're having about your college experience, and you can change how you think about those grades.  I wish you all the best.


Can I do a thesis project in an area if I haven't taken a course on it?

Of course you can! (I did. My advisor did. Most of my students did.)

Someone will have to agree to supervise your research, but that's true even if you have taken a course in your proposed research area.


Is it ethical to have a former student serve on my hiring committee at a community college?

Some colleges and universities have students in hiring committees, either as observers, non-voting members, or full members. In the university where I studied, power was shared roughly 40% / 30% / 30% between faculty, staff, and students. Hence it was obvious that there would be student representatives as full voting members in almost every committee.

Individual members of the hiring committee tend to have conflicts of interest with individual applicants, especially because the committee is often selected in advance. When such conflicts occur, the conflicted member should find a way to handle the situation, e.g. by observing the interview instead of actively participating in it.

The situation gets interesting with internal applicants and student representatives, because every potential student representative probably has a conflict of interest. If university regulations state that there must be a student representative, then the student repersentative may have to participate in decisionmaking regardless of conflicts of interest. The relevant principle here is that if every potential representative has a conflict of interest, then no one has.


Identity of a supposed anonymous referee revealed through "Description" of the report

If the review itself is not signed, it sounds like the unblinding was not deliberate. I would:

Reply as if the review were anonymous
Notify the editor in a separate, private message saying there may have been an error in showing the reviewer name


Appropriate topics over lunch with an invited speaker

There's always plenty of questions to ask. If you knew as much, or more than your speaker, you wouldn't need to ask it!

Questions that do not require a lot of experience in the field to be able to ask or understand and provide a higher volume of response. In addition, a lunch setting is less formal than a lecture, so you can use more open-ended questions not necessarily related to his talking point.

Here are some example questions that would apply to most fields.

What do you think is the most promising research in [the field] you've seen recently?
How did you come up with the idea behind [topic]?
Can you explain the [concept] as it was related to [the paper]?
I am a member of the [department] which is similar to your field. What have you seen in interdisciplinary topics that you find interesting?

With a specific field, you can also ask the speaker his opinion on [new concept XYZ] that you've learned about or read about.

Questions I've seen that are more "awkward" typically involve accidentally eliciting a direct yes/no answer along the way. Avoid "Do you think..." in favor of "Why do you think..."


The snippet doesn't state an objective. It's just a personal story about how you got into computers, but it doesn't say what you want to achieve (by pursuing an MS).

What you did when you were ten is unlikely to interest reviewers. Perhaps say "I've been interested in computers from a young age" but right now you're wasting a lot of characters on a lot of fluff. Perhaps you should leave this out entirely, unless how you got into computers from an early age is relevant to your current goals.

Also, try to narrow down your interests a bit. They're more likely to care about somebody who wants to passionately investigate a specific topic rather than someone who declares they're interested in just about everything. Again, consider leaving your interests out entirely unless they're relevant to your objective.


I use the following definition:

Methods are very simply, the things you did. The methods you used to achieve the result you're presenting. The could be new, or they could be existing methods.

A methodology is one level higher, a meta-method if you will. It is a method for creating a method. In other words a framework: a set of ideas and principles that can be applied to different contexts to create a specific method for that context.

So the line is a little blurry. If you're describing an experimental approach which is standard and unsurprising, you should definitely use methods. If the methods section is a part of the actual results you're presenting, you might use methodology, but only if you think it's sufficiently general.

As a policy, I would err on the side of caution and use methods if you're not sure. Using methodology when methods will do sounds pompous and unnecessarily complicates the text.


Referencing references that reference references? How deep do you need to check for "accuracy"?

While the system isn't perfect, the purpose of the reviews done by publishers prior to publication is to assure readers that what is said in a paper can be trusted. Some reviews take a long time and some papers require several iterations to reach this point.
So, in general, you should be able to trust what you read in reputable journals. Other journals, not so much.
But, mistakes happen and sometimes group think can interfere. If you have a reason to doubt something, then investigate it further. Perhaps that is by following references, and perhaps it is by looking at orthogonal sources. But the judgement is yours to make.
For a student, getting in to the game, however, the judgement can be in favor of deeper study rather than trust. If you don't understand something in a paper it is probably a bad idea to quote it in another. If you misunderstand something, you may also misunderstand its implications. So you look deeper until you begin to get the insight(s) that the chain of authors had earlier developed.
Trust, but verify.


Changing mailing and e-mail addresses as corresponding author--which to include?

I agree with you and shan23, it doesn't really matter, but the newer is probably better.
Well, to be bluntly honest, I tend to have a negative a-priori when I see an author of a paper with a gmail address (especially when I review it, when it's not double-blind). I know it's stupid, because it should only be about the quality of the work, but I can't really help it. Mostly because I know that there is no authentication with gmail address (I potentially could get an alan.turing@gmail.com address). I think it's ok to give an address that will change, after all, few people spend their entire career in the same institution.


How to mention a completely rewritten article in PhD thesis?

because I didnt want to give a Journal the copyright of a part of my PhD thesis

Have you checked the copyright agreement? Various academic publishers explicitly make an exception of their exclusive right of publication of the material (although graphics might be a different question) for the author's educational theses.

  Would you recommend to let the reader know that the ideas of this chapter have been published in a journal?

Yes, this is absolutely required. Otherwise, you are committing self-plagiarism, which is considered a form of academic fraud. This could have severe repercussions during your later career. The reason is that if no citation is given for something non-trivial and substantial, the reader will assume it is new and has not ever been published before it appeared in your thesis.

A good idea to handle this is to add a remark in the beginning of the respective chapter(s) that says that the following text is partially/largely based upon your journal article.


What are the differences between a PhD in Statistics and a PhD in Applied Math?

Short answer: they are two different (but overlapping) subjects.

Medium answer: Applied math is a broad term that can mean anything from mathematical physics to machine learning to cryptography to numerical analysis to biostatistics to...the list goes on. And it can mean different things at different universities/departments. There is plenty of applied math that doesn't involve statistics. I would go as far as to say that less than half of applied math involves statistics, although the prevalence of statistics is growing. And even though, philosophically speaking, statistics may be a form of applied mathematics, there are plenty of subjects within statistics that are not what people usually refer to as applied math.


From my limited experience of having worked both in Norway and the UK, I get the impression that there is less pressure in Norway than in the UK. Given the vast difference in population, it is however only natural to expect more competition in the UK than that in Norway. Also Norwegian policies seem to be more welcoming to third-country nationals.

I would however disagree that spending more time writing proposals or trying to do research that can be published quickly and get funding are necessarily opposed to anything that contributes to experience. In fact, your productivity tends to increase when you have less external pressure to dictate what you need to do.

So a place where one can thrive is not necessarily country-specific, although for some, it may be.


Austrian PhD without undergraduate degree?

I would argue the opposite way. An Austrian PhD definitely qualifies as PhD internationally. The former master curricula were typically composed of two parts that resemble the undergrad and graduate master studies. So in essence, in order to get an Austrian PhD, you need to pass undergraduate, graduate master and a PhD curriculum, while in American standards, you just need an undergrad + a PhD program. I don't see, why this should be worth less. Besides, the PhD curriculum is distinct from the others in both cases since it typically involves research, publications and conference or workshop presentations. So a PhD degree in one country also matches a PhD degree in another just by the competence you gained in addition to exams.

I don't have the exact comparison in terms of credit/effort or something like that. Maybe someone else can clarify.


What are the duties of the reviewer when reviewing a literature survey/review paper?

If you are new to this, ask the editor of the journal for guidance. They probably have some prepared.
The minimum is to make a judgement about whether you think the paper should be published at all. If it is obviously sloppy or incorrect then you don't really need to do more than say that you think it can't be salvaged.
But, to serve both the journal and the authors you can, for reasonable papers, provide any advice that you think will (a) be required to make the paper come up to the journal's standards and (b) improve it for readers.
For a review of the literature you can point out that parts are missing if you notice that and possibly provide some pointers. But your job isn't to complete the paper.
This can include some minor suggestions on the writing and on the quality of the images. But you aren't expected to be a copy-editor. But if the language is terrible, you need to say that and, if possible, say how the author might go about getting it improved.
There are very rare cases, say in mathematics, in which the paper contains a poorly written but very important result. Then you, the editor, and the authors have the possibility of getting something important out, even if it requires a lot of work. For such things you can make more extensive suggestions if you have the time.


Supervisor submitted without consent of co-author postdoc. Postdoc also submitted to another venue with consent of supervisor. Plagiarism problem?

I cannot really judge any behaviour, but a couple of things popped out for me:

Your advisor submitted an article without letting you know
He put his name as first author
He is now suggesting to keep the one with his name as first author and withdraw the one with your name as first author

I personally would write a letter informing the first conference that the submission was without your consent and ask for their policy. I would then write a second letter to the second conference informing them that the same article was submitted without your consent to another conference and attach the first letter. I would also write a third letter to your advisor with a copy of the first two letters.
Note, this is a "nuclear option" that will likely destroy any relationship with your advisor. But, if your supervisor truly stole your work as you describe, I assume this relationship is already ruined.


My undergraduate supervisor is giving me very little help

Let me suggest polite collective action. Have a group of you, maybe three, go to the prof during some scheduled time and just present the case that you need more direction and ask them to find a way to provide it. Or alternatively, a way to be a success without it.

Try to present it as a need, not as a complaint. The prof may also be dissatisfied with the amount of supervision they can give. You are generous in your assessment, and this will help. But the prof does owe you proper supervision under the circumstances you describe.


Citations in graduate school applications

I need to use facts and statistics in my essay.

You should always indicate the source of your facts and statistics. That means you will need to use citations. Which format to choose? The social sciences typically use APA, MLA, or Chicago Manual of Style. They are very different: MLA uses in-text citations while CMS uses footnotes. Use the one you prefer and be consistent. It helps to make a good first impression, but of course even a perfect mastery of style will not get you accepted. That depends on the quality of your analysis, so focus your efforts on that above all.


Is it ok (ethically speaking) to rename features of a dataset for publishing?

There is nothing unethical about renaming features unless you do so with the purpose to mislead or fabricate results. It makes perfect sense to rename features to keep a company secret.
However, a publication stating (for example): "I have some features and use them to predict manufacturing errors with 99% accuracy" has no value whatsoever: for all the reader knows you could be using the phase of the moon, dice rolls, and the position of tea leaves in your cup. The reader would be unable to tell what is going on, and unable to verify, reproduce, or use your results. This defeats the point of publishing and the paper would probably (and hopefully) not be accepted.
If you wish to publish something else, such as a new algorithm, it may be possible to use an entirely different dataset. You can still mention the actual application you worked on and simply explain that these data cannot be shared.
Also, you may be underestimating the ingenuity of others and the power of data. Are you really sure that renaming the features is enough to prevent others from deducing what is going on?


Do instructors have the right to know how many students test positive for COVID-19?

In the university I work for that would make no difference: everybody physically present is tested negative, as those who are tested positive are not allowed to enter the building, and this is checked.
The bigger problem I see with giving this information to lecturers is with smaller courses. It would be very likely that anonymity can no longer be guaranteed. Moreover, there is no clear cutoff point that distinguishes between small and big courses. So I understand the universities that do not give that information.


I worked in a specific direction without communicating it to master's thesis advisor, problem?

It isn't a problem unless you make it a problem. I would think that what you have done shows initiative and would be praised normally. That should be true even if the committee suggests that you go in another direction for the thesis.
But, to me, at least, saying that you have been exploring one of the options seriously would be a point in your favor. But if other considerations are such that you should be taking another direction now, you can do that, and not insist that you follow up now on your current direction.
If they suggest a different direction, just put the recent work away for a while. You might have the opportunity to develop it further later and the experience of doing it might actually help in following up on the suggested direction.
As long as you don't fight with people, who might have good ideas as well as authority over you, then you should be fine. Maybe better than fine. Initiative is a good thing.
Likewise, a quick update to your supervisor on your recent activities should not be an issue as long as you are flexible.


Job Market paper: what are the criteria?

I agree with @AlexanderWoo--ask people in the field that you know.  However, this also seems like a situation in which it might be useful to construct a new paper that combines material from the first and second paper.  Don't make it too long, though, and get people in your field to give you feedback before sending it, if possible.

You also might want to use different papers for different applications.  Think of this as a an addendum to the answer you referenced.  If you're applying for a postdoc, is it a postdoc with someone who is working on similarly technical material, with a lot in common with your research?  Or are they hiring a postdoc because they lack expertise in your area and need someone in that area as a collaborator?  If you think that the people likely to evaluate your application are capable of understanding paper 2 on its own, then maybe you should send it.  If not, maybe it would be better to send paper 1, or the hybrid paper I suggested.


Mass (spam) emails seeking short term internship, solutions

What I do is to provide on my web page a very explicit set of directions for how to contact me about possibly doing any kind of work with my group. I have separate sections for undergrads, grads, and postdocs. For undergrads, I explain a bit about what we do in my group, describe what undergrad research in the group is like, ask them to answer a few questions about what draws them to our work in particular, what they hope to gain by working with us, about their skills and background, and about their general interest and experience reading primary literature. I also ask for a transcript. You could ask anything, though.

With something like this in place, you can either ignore with good conscience any emails that fail to address these questions, or you can send a brief form-letter response asking that the applicant address these questions in order to be considered for a position.


What accounts for a good PhD experience?

I don't think I've ever met a PhD student perfectly happy with their work, but there is a clear pattern among the few I knew who were doing quite well: a good work relationship with their PhD advisor. This means:

Shared interest in the topic and shared specific goals (it seems obvious but it's not always the case, far from it)
Good communication, and especially mutual understanding on how the collaboration works:

agreement on the balance autonomy/supervision, i.e. what the PhD student is supposed to do on their own vs. what they are supposed to ask their supervisor advice for.
clear communication policy: emails or meeting, meetings frequency, open door or scheduled appointments, etc.

It's a matter of finding the right way to work together between the student and the advisor. For example some advisors expect their PhD student to be quite autonomous, others prefer to be involved in every decision; both styles can work, as long as the student and the advisor are on the same page.

There is no general objective way to evaluate a PhD in progress, this is why good communication with the PhD advisor is essential since they are the only person who can give this kind of feedback. If the relationship works smoothly, the PhD student can be confident even when problems happen and doesn't waste too much time and mental energy questioning their own work.


Is "Actes de JADT" same as JADT conference? Where to download Actes de JADT publications?

From here I would understand "Actes de JADT" to mean the proceedings of the JADT conference. Typically, a conference and its proceedings go hand-in-hand. Someone might informally state that they have had a paper accepted or published in "Conference X", but a formal citation would later point to "Proceedings of Conference X" or similar (the title can vary). While I have no direct prior knowledge of JADT, I'd expect it to be the same case here.

Now, clicking through the google scholar link to the actual document, it appears to be a thesis (or project report as you state in the comments), not a published article. However, there's this paper from Actes de JADT 2010 by different authors, but with a quite similar title. I think that other works may have miscited one of these, or that Google Scholar might have misinterpreted some citations. Anyway, given that your title is not listed in the Actes de JADT 2010 Table of Contents, I think you can safely assume it wasn't somehow published there.


Viewing MathJobs Applications as Living Documents?

You can edit documents after submission, but there's no guarantee that the search committee will see your edits.  Some people might start reading them as soon as you submit, even if it's before the application deadline.  Or some others might download or print out the applications for later reading.  But in either case they might not check back later to see if there have been updates.  MathJobs doesn't automatically notify the committee when you make an update, and even if did you can't expect the committee to reread your application every time you make a change.

So it is best to wait until you are satisfied that the documents are in a "final" form.  If you do find a serious error or need to add something, you can, but it's possible that the committee will still work with the original erroneous / incomplete version.

You don't need to wait to submit your application until all letters are in.  Most search committees would probably just wait to read your application until the letters have been uploaded.  Or, if their process is to read the application separately from the letters, then they could start reading the application right away and then read the letters after they come in.


Advisor wants me to come up with a research project. I came up with a project, but it's not with him

The best solution would be to meet up with your advisor and discuss regarding this matter.

As your advisor instructed to find a research project, you did. The project is relevant to your mentor but you are unsure whether your advisor would be interested in the project.

This is a legitimate doubt that only your advisor can clarify.


Missing funding deadline for serious reasons: what to do?

Of your options, I can think of no reasons not to try option 2. The worst thing that happens is that they say no. Option 1 is probably not going to work unless the deadline was missed by less than a day.

What your friend should do/should have done is emailed the committee as soon as they reasonably could regarding their situation. I would imagine that informing the committee of their situation and asking for a small extension has the best chance of going over well. The longer they wait to turn in their application or contact the committee, the less likely they are to be accepted.


Legal or duplicate to publish results in both dissertation and journal

First it is important to state whether a thesis is published or not. In some countries theses are formaly published under an ISSN and ISBN number, in others it is a pile of printed paper that is seen by a very few. I am sure anything between these etxremes exist as well.

If you have a published paper and need to put it into your thesis, either as a reproduction of the printed version (the pdf from the jorunal) or you reset the final revised manuscript, you defintely must get permission from whoever holds the copyright. This could be author and publisher or publisher only, it varies between journals. The reason why the copyright applies also to re-typeset manuscripts is because the copyright covers any corrections the copyright holder has made to the manuscript.

In reality, I doubt many publishers care, but on the other hand it never hurts to get the permission in writing. since a thesis is usually published in very few copies, it usually is not a problem. But, if the thesis is also freely available as a pdf it may again be questionable and a too obvious infringement on copyrights.

The second part is quite tricky, is it a duplication to publish both in a thesis and a journal. If the thesis is an official  publication, then yes it would be a duplication per definition. I know some journals are very strict about these things. To be more pragmatic, I wold say that it depends on how the thesis is distributed. If it is printed in a very small number and not freely available as a pdf then publishing in a journal should be possible. But I am sure this can be controversial and no consensus exists as to what is a reasonable middle way. In my field, manuscriprs are published in a thesis with ISBN and ISSN numbers (printed in about 200-3000 copies) but not available as pdf. These manuscripts are then later improved and sent off to journals. I think journals in general tend to turn a blind eye to the cases where thesis materials are recirculated.


How to discourage irrelevant self-citation?

Did I do the right thing to discourage this practice of irrelevant self-citation?

Yes. In fact, as a reviewer, you should point out irrelevant citations of any kind (self- or otherwise), and suggest that these be removed. Conversely, you should not complain about relevant and appropriate self-citations. The issue is the lack of relevance, not the self-citing.

  Is there anything else that I should have done?

This is exactly what should happen: reviewers should call out this kind of thing, so the authors will have to remove the irrelevant citations before the paper is published. This anecdote is a triumph of diligent reviewing :)


What would be the possible consequence of concealing an incomplete degree?

I wrote about this here.

Short answer: yes, it is considered dishonest, and the possible consequences are severe.  You could be dismissed from your new program, or, if it's discovered after you finish, have your degree revoked.  The likelihood of this actually happening is hard to evaluate, but those sorts of sanctions will certainly be "on the books" and available if the school decides to enforce them.

You'll be much better off if you submit the transcript and explain in your application why you decided to drop.


Is it a common practice to do all the work for PhD supervisor?

Assuming all that you state of your supervisor is true, i.e.,

Claiming primary authorship of all of your work
Making you write grants and claiming it as his own
Refusing to start your PhD programme

Then you met up with one of the classic cases of an abusive supervisor. If that is the case, then continue no further as his student. Spare no time in moving away as you won't make much progress (at all) with such an advisor.

I feel sorry for the situation that has caused you to despise the PhD degree itself. My honest advice would be to change your advisor, not your path. If the current advisor claims primary authorship over your writings and grant proposals, then it is only a proof that you are really a worthy candidate for a PhD! Quit your supervisor, not your PhD!

Think deep and make your decision wisely, as it is yours to make.


International Students transferring between graduate programs

Transferring schools is best done as soon as possible. Your first year credits may transfer seamlessly with another university, but the farther along you get the less likely the transfer will be successful. I would find someone at the university who has experience working with international students (there might even be an entire department dedicated to such) and ask specific questions of them (eg how to apply to another program, how to transfer in good standing etc). Then be in contact with the university that you wish to transfer to and make sure that you meet all of their requirements and apply for transfer prior to dropping out or officially leaving the program that you are in. You do not want to mess with your student visa etc, so make sure everything has transitioned successfully prior to withdrawing from your current location. Moving near family is a good idea, but also make sure that if you are really moving for health reasons that your health will be taken care of there. Make sure that the student health insurance will cover everything that you need for it to cover and that you can access specialists etc in the area that you are wanting to move to. Good luck!


Query on UK visa options for South African postdoc at Birkbeck University funded by a South African organisation

Unfortunately, short of marrying an EU national, you likely do not qualify for a UK visa and there is nothing that can be done about this. This document contains the information about salary thresholds. These apply strictly, there are no exceptions. Even if your position fulfils a shortage occupation the salary threshold still applies. You will need to find some more funding, or give up on taking up the fellowship in the UK. You may also consider contacting the university to see if there is anything that can be done to help your situation.


Consider the following scenario:

  I've been working with a professor for a year now, and at one of his
  events, I presented a poster. Another professor came up to me and
  started talking, and it turned out that this professor had a very
  interesting project related to my interests. I'm applying to grad
  schools in a year, and if I can get two recommendations from faculty
  it will really help my application. Should I work with this professor
  or not ?

Students have agency too. There's a lot of context and background missing in your description that Koldito alludes to. But in general students should be free to make their own decisions about their research activities and honor existing commitments that they've agreed to.

Personally, if I were Professor B, I might suggest that the student talk to you first before deciding, but it's also possible that B did that, and the student indicated that no continuing commitment existed. If I were advising the student, I'd also suggest they clear things up with you first. I might also suggest that depending on the level of interest in the project they have with you, they give you the right of first refusal.

But this exact situation has happened to me with students (twice). They worked with me for a while, and then found a topic that made more sense to them with another professor. I wished I could have convinced them to stay, but they did well with their advisors and I was on both their committees, with no hard feelings at all.


Supervisor complaining about research work is slow and not doing anything properly. Is it possible to continue with him for long?

Sometimes it's helpful to factorize this into two questions:

(1) Are you happy with the professor? You say he "is not helping" you in your research; yet, it sounds like you've made considerable progress in a short time. Assuming he never changes his ways, do you still want to work with him?

(2) Is your professor happy with you? You have said that he is critical of your slowness, but it's not clear [to me] whether he is definitely unhappy, or if maybe he is just awkward, or maybe there is some cultural/linguistic misunderstanding.

In either case, I think you should schedule a meeting with him -- actually send an e-mail and ask him to set aside 15-30 minutes to discuss your performance in the lab. Then you can ask him directly about his comments and ask whether he is still interested in having you do your PhD with him. You can also address your concerns about him (e.g., "I was hoping you'd be able to advise me more about X; do you think we'll be able to do that in the next few months?").


It would be fine to simply write

"Dear Professor X,

Thank you for taking the time to look.

Best wishes,

JansthcirlU"


Why do computer science students working in computational biology domain need to give biological validation for their prediction?

I am always in a hurry to do the same. What I have noticed for this
  field is that if I predict something, I need to provide biological
  validation for my result. Why so?

Because this is how one knows if your results are correct and useful. A prediction is nothing if it hasn't been evaluated. The field is littered with predictions that turn out to be nonsense, only hold up under very narrow circumstances, etc.

  Is biological validation not the work of biologists?

No more than it would be if a biologist said "I just developed this algorithm, proving it's correct is the work of a computer scientist."

Beyond that, there's no reason for them to do so. "I've made an arbitrary prediction, anyone want to validate it?" is going to be met with a resounding "No" - the biologists have their own work to do.

  How can a computer science student provide biological validation for
  his/her prediction? Isn't our job just to predict?

No, it's your job to provide useful results. Validated predictions are useful. Just predictions are not.

As people have noted, there are a number of ways to validate a prediction. Existing data, or even simulated data based on known biological patterns, might be sufficient. If no such data exists, it's time to find a collaborator.

  Why do the journals want biological validation for the results?

Because anything else is just speculation.

  I did a prediction job, where I predicted some proteins to do a
  particular function. I communicated it to the Molecular BioSystems
  Journal. They rejected it saying I have no biological validation. If
  biologists are the one with the final say, then what point do we have
  in working in this domain? Whatever we predict would be questioned.

Do you know that it was rejected by a biologist? There's a number of computer scientists I know who would have rejected such a paper for having no biological validation. Beyond that, your "point" in working in the field is to generate those predictions and evaluate their correctness. The latter part is also an aspect of good computational biology.


Is it necessary to discuss the reason of the algorithm choice in my paper?

If you considered others and chose one, then it would probably add to the value of your paper to explain the choice. If you rejected some for important reasons then others would benefit from that knowledge.
But if you just chose randomly, then people will wonder if your work has sufficient value. And if you say nothing, they might wonder why.
If you compared two or more algorithms and got different results, then people will want to know why.
So, I think it is probably a better idea to say something if you can.


Yes, you can do this. You are not taking his ideas, you are using your own (note you wrote "I have a few ideas").
Basically, once a paper is published, all the ideas within becomes public knowledge and you are free to build on them. You should still cite the original paper if you are building on their ideas, but your extensions are yours and yours alone.
By the way, many authors will be quite flattered if you work on their ideas - it implies that you find their ideas interesting.


How To Professionally Address A Mental Breakdown

Ask your therapist before you do anything.  They may know something we do not.
If you have a union, they may know about local rules you need to follow.  Ask them.
Tell the faculty you have been ill.  They do not need to know the details of your illness.  Nearly all faculty know that illness, including mental illness, is a common occurrence and not under your control.


Should university administrators share official matters with students?

I think a department should share information with students that can affect them. A non-hire of faculty doesn't affect students directly unless the students were recruited to the department with the promise of expanding in a certain area, and then this fell through.

But I don't know of a single department that would make such a promise to incoming students (and certainly not undergraduates).

On the other hand, if the department experiences a shortfall in funding that means that they have to change how they fund students, then these students must be informed as soon as possible since this materially affects them.

Apart from these cases, one can certainly make the argument that sharing relevant information with students helps foster an atmosphere of collegiality and gives the students a sense of belonging. Within reason...


How to tell my supervisor that I have severe phobia of flying?

Since it doesn't sound like it's likely that you will be able able to work around it in the immediate future, I think you should schedule a meeting and just have the conversation. Explain your phobia, explain the effects, and explain that you have worked with therapists and that the problem is unresolved.

Treat it like any other health or mental health disability that will affect your ability to carry out the tasks graduate students normally do and make it clear that you will attend conferences by train or bus where possible. There are many questions about health and disability on this site and the consensus generally is that if it will impact your performance, you should bring it up with your supervisor and colleagues as soon as possible.  Since this has already become an issue, you should do that now.


I publish under a one-word name, which Google Scholar does not index. What can I do?

Google scholar is imperfect. It's based on an automatic parser, rather than human curation. I've seen it make all kinds of mistakes.

What can you do? You already have set up a profile that has the correct information. You can try contacting Google, but don't expect much from them. I doubt they have the resources to deal with everyone who contacts them with an issue. However, they are always improving their algorithm and this may get resolved.

The only other thing I think you can do is alter how your name appears on papers to conform to western expectations, as suggested in this question: I have only one name shown in my ID card. How do I write my name (surname) in research paper or article?

Overall, I wouldn't worry too much about it. It is easy enough to find your publications online and any human reader will understand that you are mononymous.


Misunderstood exam question with consequences for incorrect answer

At my institution the default way to handle this is (3 Stick with the 0 for this question). Essentially, every student is required to handle the teaching language well enough to be able to work on the test. In practice, many teachers will fall back to (2 Give them some consolation points) if giving 0 points seems too harsh. If (1 Give them another stab at it with more language context) is an actual option, that seems like a senseful way, too (e.g., in a short verbal exam). However, in practice this is often not possible in my courses, either because it would be very impractical or because the course regulations do not allow it.

Both, (4 Grade the question they answered and not the question asked) and (5 Give him / her the lowest grade anyone else got for this question), seem like relatively weird ways to handle this situation. With (5), you are essentially decoupling the grades for the student from what (s)he has actually written on the test. (4) breaks a fundamental exam concept, i.e., that the instructor chooses the question that the student should be answering, and not vice versa.

As for this:

  The student is on an important grade boundary and it could make a difference to their final grade even a difference to if they have to take the class again / can graduate on time / or even stay in the major.

As bad as you may feel if "your" grade is the tip of the iceberg that leads to bad consequences for the student, you should be aware that it is the sum of bad performances that has gotten the student into troubles. Your grade is just the last in a series, and your grade is as much "at fault" as any other bad grade the student received. Hence, I feel you are not required to take the larger picture into account.


Professor stopped responding to emails suddenly. What should I do?

You have options.

You could wait and hope. The person is probably pretty busy right now.

You could try again, but I'd recommend against flooding the person with too many mails or too much information at a given time.

You could cast a wider net and try a few other professors at other places.

You could give up.

You could use some combination of the above. But casting a wider net is likely your best option, even in combination with others.


What are the recommended approaches in selecting students to work on research projects?

Our department has a policy of matching students and faculty. The faculty write up a brief description of the project they want to pursue. The PhD coordinator meets with students to assess their skill sets and top choices for projects and a match is made. We also have a policy of switching advisers after the first year. Good collaborations usually go on past this year, others have a way of dying out. However, our department is rather small--usually between 10-15 grad students at a time.