Calculating Cumulative GPA Across Multiple Colleges?

If you are asked to self report (seems weird to me) and don't have a way to provide a full explanation then you do what you can. Some type of average weighted by credits. You are likely expected to consider post-secondary education only unless it is for admission to undergraduate programs or scholarships for such.

But, you should retain the details of the computation and how you arrived at the number in case you are ever questioned. This is especially the case if you have attended more than one institution.

But, I doubt that they are looking for only the most recent institution unless they say that. More likely they want a "complete" picture. If that picture isn't very flattering you will need to explain it, but don't leave things out.

If you produce other materials than just what fits on a form, you can, perhaps, include the GPA computation. Then, if there is any question, they can give you better instruction on what is needed.


How do I prepare for my research program 2 months ahead of its beginning?

You can reasonably guess that your research when you join the group will be closely related to the research the group has published in the past 1-5 years. Therefore, the biggest leg-up you can get is to go through their recent publications (ask for them from the professor if you don't have access to the journals from home or your current school's network) and try to understand what was done, why it was done, and what tools were used?
Reading one or two review articles in the area would also be useful.


How to Cite With Inconsistent Use of Initials

You should use the exact information which is provided on the published paper, not the real or current information of the author; even if his name or affiliation1 is change at the present time.

Moreover, the correct way of citation of each paper is provided in the webpage of its publisher and you can check how they have mentioned the author's name in the citation example (you may also download the bibtex or other outputs to be used in citation manager softwares). At least, by checking the publisher website, you will be sure how they prefer their published paper to be cited (even if other possibilities/doubts for correct citation exists).

1I know that affiliation is not mentioned in citation, but if somebody wants the affiliation of the author at the time of publishing the paper, the best source is the information written on the paper and is provided in its publisher's website.


How to write a scholarship press release?

I do not want the focus to be on myself and my accomplishments.

While many of us (hopefully) have a modicum of modesty, there will be many times in your career where it is in your best interest to triumph your accomplishments, and this is one of them. In this case, it is a no-brainer: your former professor asked you explicitly to write the press release, and you should do it. Your university home page or newspaper probably has a news section that demonstrates the type of press release you're talking about (e.g., a short story with a picture and a description of the research and/or accomplishments).

The press release will be primarily about you (if you are the only winner at your school), but you should also include a paragraph about the scholarship itself and about the college and how it relates to the scholarship (e.g., "The X Scholarship has been awarded at Y College for the past 10 years, and was funded through the generous donation of so-and-so, who graduated from the college in 1954...).  If it fits in, you can mention your professor's relationship to the scholarship and your involvement (how did she know to recommend you? Was it her impetus or yours?).

If you're concerned about how to write the press-release, I would reach out to someone with journalism experience, whether it is someone who works for the school paper, or the news-section of the school website.


Do you place endnotes (in vancouver reference style) after colons or before?

This is a relatively minor point, but in standard American English usage, footnote and endnote numbers would go after a punctuation mark, not before one. Usage in British English might be different, and individual publishers may have their own guidelines.

However, one might also ask why you aren't citing each item in the list separately; it might be more informative to the user rather than doing an all-purpose citation at the top of the list!


It's not true that just because your manuscript already has two reviews that the editor will make a decision. For example, maybe the two reviews disagree with each other, or one of the two reviews is poor and the editor is waiting for the third review as a tiebreaker. The third review is ten days overdue which is not a good sign, but you can't tell from the outside. For example, maybe the reviewer had emailed the editor saying the review will be late, and the editor is (sensibly) waiting as a result.

As for "what should I do", the answer is always the same. If you're concerned/impatient, write to the editor and ask what the status is. Otherwise just wait. The review process for your manuscript doesn't seem that long to me, so I would wait, but it's up to you.


Why do grad programs ask for date of birth?

For a grad program, age matters a little bit because of little space there is in many programs. This is true of some high profile majors like medicine though not particularly true to others like Law. Public universities are tasked with graduating people who will contribute to society given that their education is A) subsidized and B) very limited in space.

This is going to sound mean, but a 60 year attempting to enter med school is not going to be a good candidate because by the time they finish med school and residency, they are unlikely to work more than 10-15 years before health complications and/or death. But if you take a 25 year old, they will likely use that degree for about 40 years. Mind you, this is not true of all universities and certainly, private ones are not held to these unwritten rules so ymmv.


In computer science, which place should corresponding author be listed?

In computer science, there is generally no straightforward connection between corresponding authorship and authorship order. There are even some fields, especially in Theoretical CS, where alphabetical ordering is the default. In other fields, seniority of authors (which is correlated to corresponding authorship, as the most senior author is usually most likely to keep his affiliation) can be a criterion for the ordering. But that's just one possible criterion among others (like, specifically, the amount of contribution).

In some conferences/journals, the corresponding author is explicitly highlighted in the author list (e.g., Springer LNCS series). In others (most IEEE/ACM-based ones), there is no explicit concept of corresponding author. The lead author (first author) can then be assumed to be the primary contact person.


Layout for a thesis chapter describing an undergraduate course

The structure of theses depends very much on the standards of individual programs & institutions.  Your best bet would be to get a copy of a previous year's thesis in your program from your institution's library (they always keep them all).  Find one that has done something similar to what you are doing and use a similar structure (and, of course, if you refer to anything in it, cite & reference it appropriately).

For your reference, here's a general new course description that I developed for one of my courses.  Its format is heavily based on the standards of the university, so may not apply to your particular situation.


The phd advisor copied my thesis to another's

Your colleague handed her hand-written thesis to her PhD advisor.  She couldn't graduate without bribing him.  He should have had it typed out as-is, but instead he took the liberty to edit it, and added plagiarism from your thesis, then published it.

He is behaving wrongly on many levels:

He should not ask a bribe.
He should not edit her thesis text.
He should not have sent in her edited thesis as her authorship.
He should not plagiarise your thesis.

The people involved:

The advisor is engaging in severe misconduct and should be fired and criminally prosecuted.
Your colleague has been uncareful to not have complete documentation.  She must retract her PhD thesis, because she did not approve the final text and should not bear responsibility for its contents.  She is a victim of the advisor but she is at a large risk of being accused of plagiarism and bribery herself, which makes her situation tricky.
Your PhD thesis still stands.  For you, it should be easy to provide evidence of plagiarism and evidence that you were the original author, for your PhD thesis was already published a year earlier.  The damage to your reputation is much less than to the other people involved, as you are exclusively a victim.

What to do:

Make sure you keep written copies of everything you do.
She has apparently already spoken to the Vice Chancellor, who believes her.  That is good.  Go there together, along with anyone else who has been wrongly treated by the advisor, and ask what formal steps you can take to make him face consequences.
If the vice chancellor is unwilling to proceed, you might threaten with publicity, but I would not do so before.
She needs to retract her PhD thesis because the text is not her responsibility and she did not approve the final version.

P.S. The advice above may be naive.  I am from a society where corruption is not considered normal (when it does happen, it is considered a scandal) and where a situation such as you describe would be unheard of in a university.  I hope the advice is still useful and perhaps the follow-up to these incidents can help improve academic culture overall.

P.P.S. If you know anyone else who hand-writes their thesis, strongly recommend them to contact a computer-literate friend to scan each page soon after it is written and keep this backed up in a safe place.


What is a suitable job title for someone responsible for data and software in a research project?

This sounds essentially like my position: research programmer

It encompasses a lot, but perhaps 80% of it is helping researchers who know what they want to accomplish but have no idea how to get there.  It can include things like web scraping or cleaning up very ugly code, or translating a project to a different codebase, or writing simulations, or running models.  Version control often comes into play, along with data storage - I'm often teaching researchers about GitHub or S3, for example.  It also tends to involve data vis and data presentation (like on the web).

It also has an element of data science, where a researcher gets access to some data that has what they want but is too big for them to know how to work with or manage.  But I wouldn't call yourself a data scientist; it's a whole separate field with its own methods that often diverge from traditional research.

It sounds like "research programmer" encompasses everything you're doing, but sound a bit more grand and more accurate than what you're using now.  It's also one that is in official use elsewhere (in my case, the policy and think tank world), so that's a bonus.


What does it mean to have vacation time in European academia?

Welcome to European vacation regulations :-).

You are entitled to X days of vacations per year. Literally. There's no hook to it. You simply ask the employer, basically your direct supervisor (head of the group, department, dean?), and if there's no reason to say "no", they will approve it. Of course taking time off during days when you are teaching needs to be explained very very well, but if your vacation days do not interfere with teaching obligations, or similar duties, you will be given the time off. That's it.

Normally at universities, unless you have a very fussy boss, nobody cares when you take vacations time (still recall non-interference with teaching), but most people take several weeks off in the summer and people with a family also during school vacation periods (country dependent). In companies, the system tends to be stricter, you should plan any longer breaks several months ahead and coordinate with your colleagues so that it does not happen that everybody leaves for two weeks and a company stops. At universities that is a non-issue, though.

Legal vacation time means you are entitled to that time. The employer is obliged to give you that time off. Suppose they will refuse to approve your vacations when you wish to take them (e.g., when you work in agricultural sector you shouldn't leave at the harvest time). In that (rare!) case, they will have to select and offer you another period of (usually at least two weeks of uninterrupted) vacations period some other time in the year.

But there is another potential surprise for you. If you won't take all your vacations in a year, since you are entitled to that time, it will be (in all countries and places I worked, but there might be local differences) shifted into the next year when you will be entitled to the standard X days per year according to the union negotiations PLUS whatever carry-over from the last year. The regulations regarding how far into the future that contingent of vacation days can be pushed differ, but normally the carry-over is useful in the very next year in full. Sometimes you might even be obliged to take it. Because if not, the employer might have a problem - again, you are entitled to vacations. And the employer can even force you take time off in order to use that vacations budget. The reason is that they don't like the idea of accumulating and then even making use of several months of vacations in a row.

As for being in the workplace during working hours, again, regulations differ but most of the time there is at least a certain period (10oo-15oo?) when you are obliged to be there. But in reality at universities I never heard of anybody making any fuss about this (except for Eastern European universities, where it can be a matter of local department politics - but that is of no concern to your case). Think about it as a legal issue. If something happens to you at office hours (a car accident), it might be considered a work-related accident, so the employers try to counter-act that by requiring you to be in the office unless allowed not to.

Later edit:

  What does vacations mean when I will likely be spending whatever free time, rushing to finish my manuscript, grant proposals, or course prep anyways?

You structure your time. It doesn't have to be the way you describe. What use does an employer have of burned out and stressed out employees?

Even later edit:
Just for completeness, being entitled to take vacations also means that often you will be able to trade days off for salary. Usually the union contracts regulate, or prevent this, but for example when you are leaving, the employer will either compensate the unused fraction of the annual vacations budget by money, or will force you to take it right before leaving the position - during that time you will receive the regular salary up to the date of leave.


The Page Rank effect of Academic recommendations for Graduate School

I’m worried if Letters of Recommendations not coming from the same ‘XYZ’ area Professor will not help my case.

While a letter from someone who is an expert in the subject of your doctoral research is better, it's much more important that the letter writer know about your research record.

Sensible graduate admissions committees know that not all universities have faculty in every research area.  They care more about what the letter says than who wrote it.


Can you describe a required online science course that used discussion well?

The best experiences I have had in working in group, in terms of exogenous motivation, were encouraging competition: define a problem, divide your students into groups, set a time limit and give a reward to the first/best/any-criteria-you-consider group.

Live discussions/meetings can be more helpful that a forum in this sense: the probabilities of engaging in a fruitful dialog increase.

You may also want to take a look to gamification techniques:

http://en.wikipedia.org/wiki/Gamification
http://en.wikipedia.org/wiki/Gamification_of_learning

If students are not motivated by themselves, the internal pulse of "trying to win" at something may do it, gaining knowledge along the way, without having the feeling of "doing homework".


Students usually decide this based on the consequences of each option. At some universities, you can retake failed exams but you cannot retake passed exams to improve your grade. In this case, it might be worth skipping the exam instead of taking it and "risking" obtaining a low passing grade that you cannot get rid of.

It might also be that you the rules give you only a couple of chances to pass this exam, so you do not want to miss this chance. Or that you do not care about the grade as long as you pass, so you might as well have a try. Or that past exams are not made available to students, so it might be worth for you to go and learn how exams in this subject look like.

If none of the above applies (i.e., if you know you will fail anyway and are only asking whether the time spent at the exam will be worth it in terms of how much you learn), I would say that those hours would be much better spent learning the subject or doing practice exercises on your own. Surely you will learn more by doing exercises in a comfortable environment (at home or at the library) than by doing the same exercises in exam conditions.


Are there application fees for PhD positions in Europe?

This is completely dependent on the manner in which the PhD program is handled. If it is a purely research position that is applied for like a job, then there is typically no fee associated with it. However, if it is part of a "program" and involves coursework and other requirements, then there may be a fee associated with a formal application. You'll have to check the announcement of the position to be certain.


Can I ask professor to send me a copy of papers?

Yes, you can, and you should. It is not impolite (unless you actually have access), and it is not unethical. I don't think it is illegal, if you do not distribute it further, and it is certainly not uncommon.

First, make sure you really don't have access (otherwise, you risk looking a bit like a fool), then ask him. Don't make a big deal of it, just explain that you lack access and you believe he may have them, if so could he please send them.


Lie or try to explain reason of my absence during classes?

Take initiative about this, and be honest. By doing so, you can help your professor see you as a busy student who made a mistake, rather than a suspicious student who doesn't seem to care about the class (and who maybe gets caught in a lie).

Ask to meet with your professor in private. At that meeting:

Honestly explain that you have missed class three times because of your job. Even though you respect the professor and care about the course, your job has interfered several times, and you are dependent on that money for your living expenses.
Apologize, sincerely. This is for missing class, for conveying disrespect through your actions (it seems like that is part of the professor's insistence on attendance), and for [other effects of your absence on the class or the professor]. What did you lose out on, and how have you tried to make up for that?
Acknowledge that it is reasonable for the professor to fail you under this policy.

You now know that the professor has this class policy, and you understand that work is not a qualifying reason for missing class, and that three absences is an automatic reason for failure.
Because you were absent for the class when this professor explained the absence policy, you did not know right away, but it was your responsibility to find out what you missed during that class and learn about the policy in that way.

Ask if there is any way that you can make up for those absences. You would like to successfully complete this class if possible. If you can sincerely do so, tell the professor what you've already learned from the class, why you're interested in the material, and what you hope to do with your degree.
Calmly let the professor know that this is a big deal for you, but do not literally beg or (try to) emotionally manipulate the professor.
Recognize that the professor can say no. And that "no" is helpful to you: if there is no way for you to successfully complete the class this term, knowing this will allow you to focus on your other classes, research, and work.

Integrity is critical to schooling, whether you're on an academic or professional path. Professors will respect someone who acknowledges breaking the rules and apologizes. That respect might allow you to stay in the class, or it might mean they give you a fair chance when you retake the class. On the other hand, someone who evades responsibility and is willing to lie about one thing may be more willing to take improper shortcuts, cheat, or lie about other things. For your career, you do not want anyone to question your integrity, whether you plan to conduct research or enter a profession.


Is it unethical to access journal articles from Torrent websites?

Ethics is (by definition) personal or at least culture-dependent.

Personally, I think it is unethical to have publicly funded research results behind a paywall. That would make the answer to your question: No, it is not unethical to use websites like sci-hub. But that's just me and others may disagree.


Please inform details and feasibility of pursuing a second bachelor’s degree in mathematics/applied mathematics/statistics/related discipline?

Age is not an issue in the U.S.

But I would apply directly to a master's or PhD program.


It's very likely that the problem is not "we propose", it's whatever follows. Apparently you said "we propose X" and the reviewer thinks that you should explain why you propose X.


How to select between letters of recommendation

On mathjobs, you can choose which letters to send to which schools.

For research-oriented jobs, send all those letters, assuming those are the established people in the best position to evaluate your research and teaching abilities.  Five is a good number of letters.  Three is on the low end, even if that is all that is asked for.  Most people submit 4-6 letters.  (On the other hand 10 is too many.)

For primarily teaching-oriented jobs, you might try to get 2 teaching letters and 2 other letters (which can address some combination of research/service/collegiality).  At least one of the teaching letters should be from someone who's observed you teach recently.  This latter aspect is also preferable but not required for many research-schools (for tenure-track positions, not so much for postdocs, even if the postdoc involves teaching).


How does the acceptance rate affect papers decisions?

Yes.

But it would be more accurate to say that conferences have a fixed budget of papers that they can accept, due to scheduling constraints.

At most computer science conferences, every accepted paper is presented in a 20-minute talk; for a three-day conference with no parallel sessions, this practice imposes an upper bound of about 50 accepted papers.  Of course larger conferences have parallel sessions, but program committees generally do not have complete freedom to add another parallel track, partly because of space constraints at the conference venue (which is planned long before the submission deadline), and partly because major changes to the conference organization usually require input from the community.

So inevitably, if a conference attracts a large number of strong submissions, it must reject some of them.  This is generally considered better than the alternative, which is that the conference must necessarily accept some bad papers.

This answer is specific to computer science.


Is it okay to digitize/modify figures "reproduced from reference" in a thesis?

Probably, but just recall that fair use is a defense in court against being sued not a blanket permission. It's always easier to ask the publisher for permission. I don't think that tracing over a scan of the figure changes the fair use analysis at all, but you should really ask your attorney. You should always reference the source of your images whether you are tracing over it or using the scan.


There is no certain rule of thumb for determining the number of pages in a journal article. If you are asking for a sheet with all the information about it, then I think nobody here is going to be able to help you out. If you need information on a specific journal, however, then you may look into the journal's "Author Information/Instruction" page or "Paper Submission Page".

However, you should also note that there are often three different types of paper welcomed by many journals:

Short paper (least number of pages) E.g. 8 pages for IEEE
Regular paper (more pages) e.g. typically 12 double column pages
Review papers (most pages). e.g. I don't know.

However, everything depends again on publishers, including whether it is a double column or a single column format. Typically single column formats have higher page numbers than the examples given above.


What are the elements of an effective elevator pitch?

An effective elevator pitch is between 30 and 60 seconds in length. Based on how most people speak, that's between 60 and 120 words. That's not a lot of time or verbiage, as this corresponds to about one paragraph in length.

If you look at the challenge as answering the six fundamental questions (Who?, What? Where?, When?, Why?, and How?), several of them have already obvious answers (these would be Who?—You!, When?—Now!, and Where?—My PhD project!). That leaves the three remaining questions: What?, Why?, and How?

Basically, I'd format the pitch as follows:

What is the basic problem?
Why is solving this problem important?
How are you solving this problem in an original way?

The other thing is to rehearse it until you can tell it without thinking about it—either because you have a rehearsed script, or because the key points have become ingrained and recallable without much thought.

======

POSTSCRIPT: As Artem mentions in a comment below, you should have different elevator pitches for different audiences. At a minimum, you should have one for experts in your specific field, one for other members of your profession but outside your field, and then a third for "general" audiences. Having one for family and friends who want to know "what exactly is is that you do?" probably isn't a bad idea, either.


Are there any changes in NSF proposals/awards processes that are likely to be of special interest/relevance to PIs?

At the top of a recent NSF Solicitation the following note exists:

  A revised version of the NSF Proposal & Award Policies & Procedures
  Guide (PAPPG), NSF 13-1, was issued on October 4, 2012 and is
  effective for proposals submitted, or due, on or after January 14,
  2013.

  Please be aware that significant changes have been made to the PAPPG
  to implement revised merit review criteria based on the National
  Science Board (NSB) report, National Science Foundation's Merit Review
  Criteria: Review and Revisions. While the two merit review criteria
  remain unchanged (Intellectual Merit and Broader Impacts), guidance
  has been provided to clarify and improve the function of the criteria.
  Changes will affect the project summary and project description
  sections of proposals. Annual and final reports also will be affected.

  A by-chapter summary of this and other significant changes is provided
  at the beginning of both the Grant Proposal Guide and the Award &
  Administration Guide.

By my reading of the section in the PDF that lists the changes, the following might be of interest to PIs:

  Chapter II.C.2.f(i)(c), Biographical Sketch(es), has been revised to rename the “Publications” section to “Products” and amend terminology and instructions accordingly. This change makes clear that products may include, but are not limited to, publications, data sets, software, patents, and copyrights.

Plus, a minor change to the Indirect Costs section w.r.t. international participants, a minor change in the Facilities, Equipment and Other Resources listing,

A change in the definition of "New Awardee":

  Chapter II, Introduction, has been modified regarding the period of time after which an organization is considered a “new awardee”. Organizations that have not had an active NSF award within the last five years (formerly two years) should be prepared to submit basic organization and management information and certifications.

Prior funding:

  Chapter II.C.2.d, Project Description, has been revised to clarify that, in the Results from Prior NSF Support section, “prior” NSF support includes current NSF funding. This section also was updated to indicate that information should be included irrespective of whether or not the support was directly related to the proposal, or whether or not salary support was provided.

References Cited:

  Chapter II.C.2.e, References Cited, has been updated to specify that if there are no references cited, a statement to that effect should be included in this section of the proposal and uploaded into FastLane.

And various other minor changes...


Review process for comments on an article

The procedure is quite common, and frequently comments and response to comments, if significant, are then published together.

  Now my query is, why and for what purpose they are seeking response from author of paper ?

Why shouldn't they? You are actually criticizing their work, highlighting some flaws. You might be right, you might have misinterpreted their paper, or you might be plainly wrong: whatever the case, it's fair to allow the authors to reply to your criticisms and explain their point of view, if different.

  Although I have no problem with that but I am curious to know, how that author would responds to my comments on his/her paper ?

Well, there's no general answer for this: it depends on the kind of comments. Sometimes they might simply acknowledge the issues, whereas sometimes the authors write another commentary explaining why they think the comments are wrong. And sometimes the two parties reach a common point of view.


Is there a more positive term for "desk rejection"?

What are you trying to do?

If you've already submitted your article but the status remains "Submitted to journal", you could ask for an update on the status of review.
If you've already submitted your article and the status has updated to something like "Reviewer invited", then your article is likely not being desk rejected because if the journal was desk rejecting, they would not be inviting reviewers.
If you've not submitted your article and are wondering if they will desk reject it, you could ask whether the journal is willing to consider your article.


Getting a job in industrial math with only a Masters?

Students with master's degrees an applied mathematics (and statistics, OR, actuarial science, mathematical finance, etc.) often find work in industry doing applied mathematics, but this work is not typically "research" of the sort that results in publications in research journals.   If you want to do publishable research, then complete a PhD.


Research partner switching authorship before publishing to Arxiv?

Make sure this is actually malicious.  If so Contact arXiv.

For co-authored papers every author should be an owner of the paper. Usually, the person who submitted the paper gives the other authors the password. It sounds like that will be problematic in this case, but you can claim ownership of your paper without the password through the arXiv system.  (This will require manual intervention from someone at arXiv.)

On the contact form there you should probably explain exactly the situation.  They are going to be the only ones who can properly address and sort through what is going on.

Needless to say, you should make absolutely sure that this rogue coauthor is intending to do this and it is not some sort of mistake.  It seems like extremely odd behavior since the paper is already submitted with the correct authorship, so it's quite easy to prove he has changed the order.  Also, once you bring this to the arXiv's attention it could have consequences for this coauthor, such as getting banned from submitting papers, etc, so make sure the act really is malicious before doing this.


How to evaluate a thesis based on papers with multiple authors

Let me start with a story.  At Harvard, before a PhD student is allowed to schedule their oral dissertation defense, which (as is the case in many places) is usually a formality, the advisor is required to explain the significance of the dissertation work at a faculty meeting, and the faculty have to agree that the work is significant enough for a dissertation for the defense to go forward.  The possibly apocryphal story goes that, after a contentious faculty meeting at which a dissertation was grudgingly approved, the advisor, a well-known mathematician who has had many students, remarked, "Well, this isn't the worst dissertation I've written."
The point is that, while we claim that a dissertation is the work of the student, in most cases, this claim is really partially true polite fiction.  Certainly the student is expected to understand all of it, and to have contributed significantly to it, but, in any sort of collaborative theoretical work, it doesn't even make sense to precisely separate out which ideas came from whom.  I've heard mathematicians claim that they correctly decided which idea to pursue to solve a problem based on the quality of the silences during a conversation with their collaborators, and I believe this claim.  When ideas are developed with such subtle yet vital contributions, it makes sense to just give each co-author 100% credit for the ideas.
Unless you have a policy that theses should not be based on collaborative work - and, frankly, this policy is unenforceable due to the common but not universal custom for advisors to decline co-authorship with students on papers where they would otherwise be a co-author - you really have no choice but to take at face value the claim that the thesis represents the student's work.  At the least, you can expect the student actually wrote the text of the thesis and understands its contents, and if there is an oral defense you can test whether this is true.  Beyond this, you will have to trust the student and the advisor that some acceptable portion of the ideas in the work actually came from the student.  Someone contemplating hiring the student will get more information in the recommendation letters from the advisors and the other collaborators.
It's generally understood that an advisor usually ends up spending more time advising a student on solving their dissertation problem than it would have taken the advisor to solve the problem themselves.  You might want to read between the lines of the following statement about the culture of PhD advising from the American Mathematical Society: http://www.ams.org/about-us/governance/committees/Statement_DirectingPhDTheses.pdf


A paper I received to review has (independently) duplicated work that we are writing up. How to proceed in light of peer-review confidentiality?

Your question raises several quite serious ethical questions - thank you for posting it!

From the last part of your question it looks to me that you actually do have a conflict of interest, since you are afraid that what you write in your review may impact your future relations with this research group. I think it is best for you to withdraw from reviewing this manuscript, and fully explain your decision to the editors. I would even consider sending them a draft of your manuscript, if this does not violate your arrangements with other authors.

I am not sure your own paper can not be published. In my area it is not uncommon for two groups to produce similar results almost simultaneously (the second paper is submitted before the first is printed). This does bring some hard discussions sometimes, especially if the ideas are published on arXiv or presented at conferences. However, this does not stop papers from being published. Of course, you should not use anything from paper B to improve your paper A.

To summarise: In my opinion, it's best for you not to study paper B in too much details, withdraw from reviewing it, explain this decision to Editors, and continue working on your paper A.


This depends entirely on your field, and specifically, what the norm is in your field. In mathematical fields like statistics, economics, physics, and math itself, and to a slightly lesser extent in chemistry and computer science, using Greek letters as variables is exceedingly common - in fact, it's unusual to see a paper that doesn't use a few, and there are many quantities for which the well-established standard notation involves a Greek letter. In other fields, perhaps that's not the case.

If you're still not sure after examining the norms in your field, I'd just go ahead and do it. Given that mathematicians use Greek letters all the time, it stands to reason that when you are doing math in another field, you should be able to do so as well.

However, I would caution you about one thing: try to make your variable names descriptive. That is, it should be easy for the reader to make the association between the variable name and what it represents. So when there is a standard notation for some quantity, use that; when there isn't, subscripted symbols like "t_scaled" are one good way to do it. They do take up more space on the page, though, and can make formulas look unwieldy, so you have to strike a balance between aesthetics and clarity of meaning.


Is it normal to have grad student instructors for upper division classes?

US News and World Report has data from 697 ranked colleges. Of these:

544 schools (78%) reported that no graduate students were the primary instructor of any course. These include all except two "National Liberal Arts Colleges."
The 10 schools with the most graduate students as primary instructor were all large public research universities. These 10 schools reported that 18-26% of their TA appointments were as the "primary instructor."

Purdue University is listed as the school with the highest fraction of graduate students as instructors of record. Their policy allows the department to assign courses to graduate students; it makes no reference to upper division or lower division.
As another case study, the University of California reports that "as students progress through their academic careers and enroll in upper-division and graduate classes, they receive more consistent exposure to full-time permanent faculty and smaller classes." More specifically, the policy at Berkeley allows graduate students to teach lower-division classes, but they do so under the supervision of a faculty member, who remains instructor of record. However, Berkeley does allow graduate students to be the instructor of record for an upper-division course, though usually in exceptional circumstances only.
Summary: about 80% of universities do not allow graduate students to be the instructor at all. Of the other 20%, most are large public research universities. There is less data about the courses to which these graduate instructors are assigned, but Berkeley is an example of one school that will "formally" assigns graduate students to upper-division courses but not lower-division courses.


What happened to the Piled Higher and Deeper comics?

According to the latest comic, the series is on hiatus until November 2019. The unsubtle message behind the comic is that the author doesn't owe an explanation to anyone.


What percentage of phds in math actually get a tenure track academic job?

No. No one single factor guarantees you an academic job in a top university.  Whether or not you land such a job is a combination of many things.  These include,

talent
hard work
motivation
quality of research
quality of teaching
ability to network and get along with people
ability to communicate (both orally and in writing)
success in securing external funding
luck.

If you want such a job, here's what I recommend.  Choose an area that you're passionate about, go to the best school (most challenging and "highest rated") that you can get into, and work with an adviser with a strong publication record.  At each step along the way, surround yourself with (and learn as much as you can from) the most successful people possible.

You can find a partial answer to your question about percentage by reading the annual Survey of the Mathematical Sciences (by the American Math Society):

http://www.ams.org/profession/data/annual-survey/annual-survey


The Importance of First Impression in PhD Applications

In the US, few entering students have much in the way of research. The usual case is that students enter doctoral programs without an MS or the equivalent. The earlier education is broad, not especially specialized. So, in the US, lacking research credentials should not be an impediment, provided that other things in your background point to success.

The situation in Europe is quite different as the undergraduate program there is more specialized. I'll let someone with more experience there answer for the EU. I suspect, however, that a few papers would be looked upon favorably.

But the path may be longer in the US, with some coursework prior to qualifying exams. Five to seven years past the BS is fairly typical, with the early part, again, not particularly research oriented. There are exceptions to this, of course, and it is possible to enter at a more advanced stage as long as you can pass the exams and find a suitable advisor.

And note that in the US, it is relatively uncommon that you enter knowing who your dissertation advisor will be. That choice is normally made later after you have narrowed your field. So a "first" impression with the advisor depends less on your CV at entry, and more on how you do in the first years.

But the question you actually ask (mediocre, first impression,...) is more subtle. You need an excellent CV and Statement of Purpose along with letters of recommendation. It is just more likely to be light on research in the US.


What is the best way to provide an erratum to the public until the journal publishes it, or if it does not?

Publish a technical report / preprint without the error.


How to say "I'm not interested" in a polite way?

Simply saying that you are more interested in the earlier research direction ('topic A') than the current one, should be fine. Thank him for getting back to you, but you don't need to say more.
No need, of course, to say you think that the new topic (B) is boring. But "Thanks" is all you need to express.
One thing that might happen is that you get a reply containing some lobbying for you to join. You should listen, but have no obligation to accept any offer, of course. The person might be a valuable contact in the future, even if you are in a different area.


PhD study (University accreditation) and the ability to teach in the USA

Accreditation is supposed to enforce standards of quality in higher education institutions. If an institution does not have accreditation, then it is extremely suspect, and any degree you obtain from it is likely to be completely worthless. This is from the Wikipedia page on unaccredited institutions:

  All fraudulent diploma mills are also unaccredited schools, although they may claim accreditation from an unrecognized agency. Accreditation from such organizations, known derisively as accreditation mills, is unrecognized by any government or reputable private entity, and any courses taken or degrees received from such a school are generally considered invalid.

As you noted, the "university" claims to be accredited by the "International Accreditation Organization". This has the hallmarks of an accreditation mill as described in above.

I would be extremely wary of this particular institution, and it is unlikely that any other academic institution would hire you on the basis of a degree from it.


Computer Science, MEng or BSci + MSc in the UK?

Short answer: They are viewed as both roughly equivalent. MEng (or MSci for other sciences) is a 4 year course. BSc + MSc is 2 course (3 + 1 years).

Longer answer/other useful info: I studied an MSci in Physics not CompSci so there might be some minor differences between the subjects, I don't think they are significant.

Although not directly asked I also feel its import to point out that MSc and MSci in the UK are different (MSc is one year, MSci 4years).

Generally in the UK a single 4 year course is becoming more popular. Of my physics course ~60% did the 4 year MSci, ~10% did the BSc and then an MSc somewhere else and the rest only did the BSc. Now these numbers are only an example and details will depend on course and institution (many lower ranked uni do not offer a combined course).

In terms of content both options are likely to be similar. Possibly the BSc and MSc tends to be slightly more research/project based. Although this is very course dependent. I recommend you research the course syllabus for each option.

The main factor to recommend the MEng is funding. For UK students student loans are generally only available for your first degree. This means subsequent 1 year masters must be funded independently/by a bank loan, which is often prohibitive for many people. As you are a Spanish student I am not sure what the situation is for you. Obviously this is something you may want to consider.

In favour of the BSc + MSc it offers more flexibility. You can chose a different institution or a more specialized course after your BSc. The flip side is you are not guaranteed a place anywhere. Additionally many jobs do not require a masters so it gives you the option to only complete the BSc (someone else might comment on how true this is in CompSci).


Paper accepted in journal, should I remove style file for arXiv preprint?

Legally, the style file at first only is the software which you use to generate your paper and thus there should not be any problems in most cases, for the same reasons that you do not need to ask Microsoft for permission each time you publish something generated with Word. I see three problem cases, however:

If you use TeX, and ArXiv does not have the style file and thus you need to supply it, which would make it be published alongside your article. In this case you may be distributing a software that you are not allowed not distribute. In my experience, many style files are free to distribute though; have a look at it whether it contains some license.
The style file includes a logo or similar (e.g., Royal Society Publishing’s style file does this), which in turn may not have a license that allows you to distribute it and also probably is a problem because of the next point.
The style file makes your paper mention the journal’s name, publisher, or similar, which creates the false impression that your preprint is actually a publication of that journal.

Will the journal get mad? – Of course you need to regard the journal’s copyright agreement (which you accepted) with respect to publishing preprints in general or on ArXiv in specific (Sherpa Romeo is a database that helps you to find this out). But if the journal allows you to publish a preprint content-wise, I do not see any reasons why using its style file would enrage it, given that the above problem cases do not apply. Some journals even allow you publishing the journal’s version of the paper on ArXiv, e.g., the Physical Review series.
Finally, a stylistical argument: If the journal has a single-column layout but your paper has no long equations or something else that would make such a format a good idea, you may want to opt for a two-column layout for your preprint.


Ethics of scraping "public" data sources to obtain email addresses

A relevant guideline from the Council of American Survey Research Organizations' Code of Standards and Ethics for Survey Research:

  Research Organizations are required to verify that individuals contacted for research by email have
  a reasonable expectation that they will receive email contact for research. Such agreement can be
  assumed when ALL of the following conditions exist:

  A substantive pre-existing relationship exists between the individuals contacted and the
  Research Organization, the Client supplying email addresses, or the Internet Sample Providers
  supplying the email addresses (the latter being so identified in the email invitation);
  Survey email invitees have a reasonable expectation, based on the pre-existing relationship
  where survey email invitees have specifically opted in for Internet research with the research
  company or Sample Provider, or in the case of Client-supplied lists that they may be contacted
  for research and invitees have not opted out of email communications;
  Survey email invitations clearly communicate the name of the sample provider, the relationship
  of the individual to that provider, and clearly offer the choice to be removed from future email
  contact.
  The email sample list excludes all individuals who have previously requested removal from
  future email contact in an appropriate and timely manner.
  Participants in the email sample were not recruited via unsolicited email invitations.

It would seem here that GitHub users do not have a reasonable expectation that they will be contacted for research.


Is job experience more valuable than taking more courses?

If the "job experience provider" would write a good recommendation for you afterwards (surely you must also deserve it), this may matter more.

Unless you skip some very basic course that your future company sees as very useful for your work. For example, if the future company focuses on C++ development, a course with good marks in C++ programming may matter more than work in some company that required HTML/CSS only.

I would say, take that job but think well which course deserves dropping most of all.


Is it ethical to post (part of) my research question on the internet?

Posting questions is ethical, the issue is with appropriate credit and potential collaboration. I would say that  most answers will be directions to published work that covers your question, if the question is about problems already solved. In this case, you just have to reference the books or papers that you used.

If it turns out to be an open question, it probably won't be answered in a simple post on internet sites. In this case, in the best scenario, you could find people that will collaborate with you in a more permanent way, till you both solve the issue and, eventually, publish a paper.


Inappropriate reference requests from Journal reviewers

If you think you see this often, imagine how much more often journal editors see it.

So sticking to ethics is fine. Journal editors see this often enough to know when to reject a review because of it. You are not generally under threat of rejection if you decline to cite a reference. The worst that can happen is that the reviewer rejects your article, but since they've already recommended revision the first time, the editor is more equipped to discern if the rejection is unfair. Remember that if the reviewer says "reject because they didn't cite XYZ", the editor (who is able to see the reviewer's identity) is very much able to see if XYZ is also written by the reviewer. In your case you even have an editor who said to refer any inappropriate citation requests to them.

A word of caution: there's no guarantee that the requested citations are articles by the reviewers. There's a lot of diversity in what reviews look like, and it's possible the reviewer did not write those articles. Don't leap to conclusions. Stick to the facts ("we do not think these articles are relevant") and don't allege collusion (such as how the reviewers & editors are from the same institution - you simply don't know).


What does referee mean in The Computer Journal?

The editor works for the journal and recommends changes to the article for clarity and organization. He or she also makes the final judgments regarding if and when an article is published. The editor does not evaluate the work technically in the same way that referees do. The referees are peer reviewers who are deeply familiar with your field of work and will evaluate your article for its scientific merit. To have your article published, it must be approved by both the editor and the referees.

For a further explanation of how to suggest referees, see the accepted answer to this question: What is a referee in the manuscript submission process?


IRB (Institutional review board) : Do journals ever check? Does anyone ever check?

I have never heard of a journal checking for IRB approval. However, as @xLeitix notes, your university may care very much, since doing studies on humans without IRB approval may get it into legal issues.

And I personally know of one case where departmental colleagues initiated a scientific audit of a professor, requiring her to dig up all documentation (filled-in questionnaiers, raw data, ... and IRB approvals) for some studies they were concerned about. Everything checked out all right, but if the IRB approvals had not been there, the PI would have been in very deep doo-doo.

So: get your IRB approval, and make sure it's safe and sound, with scans and electronic backup. Keep it for the requisite number of years, even after the study has ended and been published. Inquire of your university how long that is. Given today's cost of storage, I would keep the scan around indefinitely.


Why don't Universities pay PhD students more?

For students funded via the NIH and similar mechanisms (CDC and AHRQ come to mind), there are standard rates for what graduate students are paid. This is a fairly extensive treatment on the subject for one university: https://controller.ucsf.edu/file/4361

There are some ways to supplement this, but "This is what my grant pays for" is a very strong pressure on budgets, and departments often set grad student pay by policy in light of this, to prevent there being clear gradients of funding between students in their department.

Note that going over this by a lot via something like unionization can have extremely unintended consequences, like PIs suddenly becoming much more interested in postdocs.


PhD crossroad: dealing with constantly absent supervisor and diverse workload?

It's not clear to me whether you did Step 1 (or Step 2) yet.  Forgive me if you already did them.

Step 1. Talk to your advisor and let her know how much time per week (or a percentage or proportion  of your time) is being spent on the project, and ask for help and/or advice about how to balance your time more effectively.

Step 2.  Work in the library, work at home, but limit the amount of time you spend in your office where other project members can grab you or distract you.


Importance of domain selection for undergrad applying to a PhD program (USA CS)

Actually, in the US, any research experience at entrance with a bachelors is a plus, possibly a big plus. Having an idea of where you want to go in research is a big plus, even if not entirely settled. So, yes, it is good to mention the specific areas that most interest you and any experience you have with those.
But acceptance depends on many things, from GPA to letters of recommendation.
I'd suggest that, other things being equal, having an idea of what you want to do in grad school will be an advantage and will help you choose more precisely when it comes time to do so.
But doctoral studies in the US normally start with a lot of advanced coursework leading up to the comprehensive exams so that candidates have a fairly broad exposure to mathematical concepts even before they specialize (and specialize...) on a dissertation topic.
It might be a mistake, however, to refuse to consider other options. Keep an open mind. You will have plenty of time to develop a formal plan.

My own experience was that, at entry, I would have been pretty happy with anything in analysis or topology, but nothing specific beyond that. And pretty unhappy with algebra. My only "research" experience was in the philosophy of math and it was pretty embarrassing. Long time ago, however.


Can a Master student's thesis be kept indefinitely until the advisors have extracted everything the student has to give?

This is not strictly speaking a legal issue. There are generally internal university regulations that govern theses and dissertations, but enforcing them is not something that can be compelled through force of law.

There is normally a limit on the amount of time that can elapse for changes to be demanded, but this is entirely institution-dependent. Usually, though, any such period coincides with the conferral of the degree. At that point, the advisor and committee cannot ask for more changes.

All of that said, someone has committed derilection of duty in advising you. If there was a question about whether or not you were ready to defend, it should have been addressed before you wrote up the entire thesis and scheduled the defense. (It may have been the responsibility of a thesis committee, not the advisor, to make this decision. I don’t know without knowing more about the departmental regulations.)

Right now, I would talk to the other members of the committee, the chair of the graduate studies committee, and the chair of the department to figure out what can be done. This is not a good situation, and if your defense is scheduled for the near future, you may need to postpone it at least temporarily to avoid problems if your advisor is deadset on you redoing everything.


Can I rewrite sentences after my article has been accepted, when reviewing proofs?

The key word in your question is "some."

If "some" refers to a small number (less than about 10), and the "rewrites" are relatively minor, this should not be a problem. On the other hand, if you have an extensive list of changes spanning multiple pages, and the changes affect the interpretation and argumentation of the article, then the publisher will likely balk at making all of the changes without obtaining editorial approval


How should I write literature review for a paper that is an extension of my own research paper?

I think the best approach is to think of them as two completely separate papers. When you write the second paper you should write it as if you have read but not authored the first. You therefore need to add the necessary background and literature review to make it stand on its own. The reason for this is that anyone who finds your (second) paper once published will not necessarily know of the connection, may not have read the first, and will need a reasonable introduction to the subject.

So, each paper should be an entity of its own. The only clear case where this may not be necessary is if you publish two papers back to back as part 1 and 2 of a series with the same main title but differing sub-titles. Then it is clear that the papers belong together and you may expect people to note and read both papers to a larger extent.


Pointing out language mistakes in a review

If a reviewer has problems to follow the arguments and feels that this is due to the use of English, they usually include this in the review. Unfortunately, it is sometimes hard to pinpoint exactly what is unclear about the language, but a good reviewer should make some effort to help the authors. On the other hand, if the overall recommendation will be "reject" many reviewers do not invest the time to write down all unclear/wrong/misleading formulations. Note that a good reviewer may still follow your arguments although the language may be quite misleading (by just knowing what you are trying to show and correcting the wording while reading).

So you may ask for clarification (and I find this a reasonable request), but you should not expect to get an answer if the paper has been rejected anyway.


Should one update a manuscript to current state-of-art when re-submitting?

Yes, you should update your references at every possible opportunity.  Whenever the manuscript is in your hands, if it is possible for you to update the references, you should do so.  Paper rejected?  Update the references before resubmission.  Paper accepted?  Update the references before sending back the revision.  Multiple rounds of reviewing?  Update the references after each round.  Submitting a journal version of a conference paper?  Update the references before submission.  Reviewing galley proofs?  Okay, then you probably can't update the references.

Your paper serves as not only a description of your new result but also as a guide to the surrounding literature.  Your readers (including referees and editors) are best served by the most up-to-date snapshot possible.

Of course, if one of the papers you cite has undergone a revision (for example, and ArXiv preprint has appeared in a journal), you must read the new revision yourself to make sure that the cited information is still there, so that you know how to appropriately cite it.

I typically tag completely new references (for example, a relevant ArXiv preprint appears while my paper is under review) with phrases like "Since this paper was submitted..." or (since I'm in computer science) "Since the preliminary version of this paper appeared...."


Should I mention a professor's name in my SOP for MSc if the professor is only taking PhDs?

There is no reason you shouldn't mention the professor's name and your interest in his field. It will show that you are focused.

In the US, the master's degree is often (usually?) seen as a step along the way to a doctorate, so you will probably be perceived that way in any application. Also, a Master's in the US will usually not be entirely research focused and will include quite a lot of course work. You will be able to meet with him if you are accepted and can work toward some relationship with him. If you think you aren't quite prepared to work under him as a PhD student, the work toward the Master's degree should get you closer to that goal. You might also find that your goals change, of course.

Since he is a new professor he isn't likely to be tenured. This can be a problem for students as he will be very focused on his own research and work towards tenure. This means that he may have less time for students. He may also have an agreement with the university that he can focus for now on his research with (only) advanced students.

But treat work with him and his group as a tentative thing. But stating that you have an interest in that can do you no harm and may serve you well.


How to deal with results that are given as exercises

In mathematics, if you cite a result, you should really be able provide the proof if somebody asks for it. So I would strongly recommend against option 3.

One thing you might consider is writing the author of the textbook, explaining your situation, and asking if he's willing to send you a proof. Then you can cite it as

  problem 8.35 in textbook, proof provided by private communication with [author]

even if he would rather not have a proof of the exercise published.

Of course, if he replies "I think I had a proof when I wrote the textbook, but I've forgotten it now," you might need to come up with a proof in some other way.

There is at least one exercise in a textbook whose proof is highly non-trivial, and was an open problem for several years before a journal paper giving the proof was published (and the only indication in the textbook of this is that part (b) of the problem is "optional").


What should I do if a professor agrees to write me a letter but cannot guarantee it being the strongest one?

I think he is honoring you with his honesty, in fact. First, take his advice and look for another letter from elsewhere. If he is well known then his letter probably won't help you with this grant. He probably feels an obligation to support his own students to the maximum.

But you could also ask him for his advice on what to do. He would probably say the same (get another person to write).

If you do find another writer, just let him know that you took his advice and thank him for it. It will keep future doors open.

But in future, I would definitely ask him for his help with letters and advice. He has been honest enough that you can trust him and be pretty sure that he respects you in return.


According to Naric (the UK's national agency responsible for grade comparisons):

  [Egyptian undergraduate] grading systems vary between institutions and even departments. The table below indicates the different systems in use and the relationship between them:

  75-100     Distinguished / excellent / very good     A

  65-74      Good                                      B

  50-64      Pass                                      C

  0-49       Fail/Weak                                 F

For a UK undegraduate degree, grading is almost always as follows

70-100     First Class

60-69      Second Class Upper Division (often written 2.1)

50-59      Second Class Lower Division (often written 2.2)

40-49      Third Class

0-39       Fail

Naric suggests the following equivalency:

First class = A or A-

Second Class Upper Division = B+ or B

Second Class Lower Division = B- or C+

Third Class = C


Publishing open-source code similar to unfinished master's work

As long as your new project is entirely original and does not infringe any patents, there is no issue with releasing it.

It is highly unlikely your professor or old institution would possess any patents for a simple program. It's impossible for me to state anything with certainty as I do no know the nature of the software, but software patents are already fairly uncommon and legally questionable. You could look up the concept and professor's name somewhere like Google Scholar to be sure.

The primary concern would be if you re-used source from the time you were at the institution. This depends on the agreements you made with the university; if you are reusing components, you should review what you signed related to your master's program and possibly contact the institution's legal department for advice. You could of course cut out such components as well, which is what I would suggest.

The fact you learned something you later applied does not give those who taught it to you any legal or moral rights over the work. Especially considering it sounds like you did all the leg work in the first place.

If you are worried in an academic context of accusations of plagiarism, you could simply acknowledge where the concept came from / previous work in a README file. If you are not infringing patents or copyrights, there is no reason not to.


How to politely encourage academic integrity in non-academics?

Ask for another meeting. Explain politely that you were very concerned by the "bury it" remark.  See what they say.  With a little luck, it'll end there.

If you're not satisfied, you can ask for a letter explaining how they will handle any negative results and make your continued volunteer work contingent on getting a letter that's satisfactory to you.

If you don't get it, walk.  The inefficiencies you're worried about will eventually come to light, and you don't want to be tarred with that brush.

Edit: The remark from Pam to the question has very good advice for conducting the meeting I suggested.  A positive approach early-on is quite likely to lead to a satisfactory conclusion, without need for letters, etc.


Repeat dropper and failure at multiple colleges. Is a Master's ever possible?

Let me come at this from a different angle (and from someone who has faced something similar in the past.)

Why do you want a masters?  What is your goal in getting a masters and/or a PhD?

Is you goal "Because I always kind of wanted one"? Is it "Because it will help me with my career goals"? Is it "Because I want to show that I can"?

This is not to be a negative nelly, though it may sound that way, but Graduate course work, especially in Computer Science(an assumption based on your current work as a web-developer), can be very challenging and stressful. Depending on the program and the instructor, it is not unusual for over half a class to have, on paper, a 'failing' grade. Some teachers are great about communicating that this is OK and expected, other's will let you hang out and stress about whether your 'failing grade' is really a failing grade. Some of these courses can involved 20+ hours a week of project or coursework. Some have no 'right' or definite answers.

None of this is to say you shouldn't go for it. Recognizing and working on an anxiety issue(or any mental health issue) takes a great deal of strength and hard work. That you have persevered to complete an undergraduate degree shows that you are a hard working, intelligent, passionate individual.

What I am saying is - analyze your reasons for going to graduate school. Make sure that what you get out of graduate school will actually match those reasons and that you approach it in a doable fashion. I would recommend a multi-step process.

Identify the school / program you are interested in attending
Register at that school(or a school with similar characteristics) to take courses
Take high level undergraduate courses. Look at the graduate degree you are interested in - often they have prereqs that you could take. Take difficult courses that are stressful to get a feel for what graduate courses will be like.
If you have time - get involved in a research lab that interests you. Make some connections with professors(and incidentally the admissions council).
Once you've got a year(ish) of courses under your belt - go for that Masters or PhD!

Doing the above benefits you in many ways. First and foremost it gives you a safe place to fail gracefully. If you're taking a course not for your masters but as preparation then dropping it isn't a big deal. Maybe you'll find you need another prereq, maybe you want to spend some time buffing up on the material. There is a big difference in having the pressure to 'pass right now or fail forever!!!' (well, what you brain tells you is failing forever and what is, in reality, not a big deal) and 'well I could take this later once I do ____....'

Secondly this gives you a little bit of a buffer. This shows any admissions group that you can take challenging classes and pass them. That you can work through the rigors of Masters program. And you can point to this during your statement of purpose as 'proof' that you have improved your reaction to anxiety around school and have a support network/plan in place for the rigors of graduate work.

Thirdly this gives you a chance to get the admissions committee on your side. If professors and admissions officers know your name(in a positive light) it can make a real difference in how your application is received. Additionally some schools have 'backdoors', so to speak, into Graduate programs especially for non traditional students.

Finally, and I hope this goes without saying, make sure you have a support network in place. I would recommend, as someone who has been there and gotten the teeshirt, that you have a local therapist for, at least, your first few semesters. Additionally there's no shame in deciding that graduate school isn't for you(I ultimately decided that PhD papers are the bane of my existence and am not current pursuing a PhD.)


Contacting potential postdoc advisor in open announcements

Apply via the university system first - most likely you will have to do that for HR to even consider you a candidate. Then, reach out to this person and ask him or her if they can and want to receive a copy of your proposal. Some universities have rules when there is an open announcement regarding what they can receive from candidates and how they receive it (standard email versus the online submission system). Plus, if the person is swamped with work, getting an unsolicited research proposal via email may be overwhelming for him or her and not helpful for you. If he or she wants to work with you and knows that you applied, they can advocate to administration and/or committees about your merit as a candidate.  Good luck!


What should you do if you spotted a non-trivial error in a highly cited paper?

The main answer to your question is easy: talk to your advisor.

I find it a little curious that you have not done this already.  As a graduate student, you read a very famous paper (in mathematics, more than 150 citations is a very large number) that was written a while ago, and at the first sign of trouble you contacted the author of the paper.  That is already a little strange: although both are possible, the probability that you, a relatively young graduate student, have misunderstood something in the paper (or are applying standards that are different from those of the field you will be working in, or some other similar issue related to the fact that you probably do not yet have expert level knowledge and experience in this field) is higher than that the author has made a serious mistake.  Writing to someone that you don't know at all and who is much more senior than yourself and pointing out a mistake is not without risk: the risk is that you will be wrong and they will dismiss you in the future as a less than serious person.

Your advisor is there exactly for such things: she is the person who is helping you transition from a neophyte to a journeyman to an expert, and she needs to see your mistakes and flawed reasoning in order to do this properly.  Some outside expert really does not: they can wait to see the finished product that you become.  Moreover, you are presumably reading the paper because your advisor wants you to, perhaps even because she directly told you to read it.  Therefore a mistake in the paper is your advisor's problem as well as yours.  Why are you holding that information back from her?  You shouldn't.

Having said that, I feel like the OP is getting a fair amount of advice that would be more appropriate in other fields than mathematics.  Especially:

  In mathematics it is very difficult to write a paper whose sole or even primary purpose is to point out a mistake (even if it includes a correction) in someone else's work.

This is a cultural reality of the field; it is certainly not entirely positive.  In many other academic fields, one can "score points" by pointing out others' mistakes, and in some fields this is one of the best ways to score points.  Mathematics is not like this: if you can get such a paper published it will "take points away" from the author and give you a certain amount of notoriety, but if this is for instance your first published paper then many people will look at you strangely, almost as if they expect you to make further trouble.  (Again, I'm not endorsing this cultural practice; I'm just describing it.)

Similarly, I would say that contacting the editor of the journal in question is maybe step 10 of a procedure that is mostly designed to terminate after one of the first 9 steps.  You should do this only after you have exhausted every other possible avenue.

  In mathematics -- very much unlike in some other fields -- it is prohibitively unlikely that an editor will publish any "commentary/correction/erratum" by you unless she believes that you are mathematically correct in the point you're making, and convincing someone with standing in the field like a journal editor that you are mathematically correct is largely what you're trying to do anyway.

Finally, while I barely know what a white paper is and to the extent that I do I'm not sure it's the appropriate terminology here -- in content I do agree with @eykanal's suggestion: it will certainly help your advisor if along with communicating the surprising news that Famous Paper X is wrong, you can supply a written version of your arguments.  This can be hard to do: explaining why a difficult argument is subtly wrong is one of the sternest expository challenges in mathematics that I can think of.  It takes a lot to go from "I don't understand the argument and find it rather unclear" to "I am convinced that it is wrong."  By the way, in writing to an author it is a good strategy to err on the side of the former quotation.


Put a forward reference in the introduction

While these forward references are not "sexy", they help to understand the structure of our argumentation that follows. As usual, it depends on the reader if he likes it.
Be sure that your flow is a a logical sequence of (short) arguments even in this abstraction.


Are there some fields where having skills in a language other than English is necessary to perform research at an international level?

Are there some fields where speaking a language other than English is necessary to perform research at an international level?

It depends on what you mean by "speaking" and "necessary".  In mathematics, there is no need to speak any language but English and the language of the country you are working in, but there's a real benefit to being able to read other languages.  It's not strictly necessary, and its importance varies between fields.  In my case, I don't use other languages on a daily or even weekly basis, but probably read French on a monthly basis and German a little less frequently.

In my view, the reason for language exams isn't that these languages are required to be a researcher, but rather that they are helpful.  The best argument I've heard for requiring language exams is as follows.  Learning how to read mathematics in French or German is not very difficult, but it's still a burden if you just want to read one paper.  Usually you can get around it by finding another exposition, finding someone to explain the paper to you, or just deciding the paper is not relevant enough to bother with.  However, even though this is a rational solution to a one-time dilemma, it's a bad idea if you are going to be faced with these dilemmas repeatedly.  At that point, you'll gain a lot in flexibility and convenience if you can read the papers you want to read.  The purpose of language exams is to keep people from repeatedly making short-sighted choices.

I'd guess that language skills are more important in mathematics than in most scientific fields, because the mathematics literature has an enormously longer half-life.  In my work, I frequently use and refer to papers that are 50 years old, and sometimes quite a bit more.  These results have not always made it into textbooks, and even when they have the original papers sometimes contain valuable insights.


How to avoid personal issues interfering with my Ph.D. studies?

The problem is easier than it seems. Your first responsibility is to yourself. What you most need to do is find a way to build a life for yourself that you will enjoy over the long term. This could involve a PhD or not, however, you seem to really be attracted to Academia where a doctorate is required. Earning the degree might actually be the sacrifice you make to achieve your goal. But keep the "good life" rather than the PhD foremost as your goal.

A number of things in what you say indicate that you might profitably look at a different subfield than mathematical biology. You can use your current position, as well as your past education, as a base from which to conduct your search, speaking with other potential supervisors and even institutions. Don't underestimate the value of a good supervisor, of course, and she may be able to help you if you approach her in the right way.

Having been chosen, rather than choosing is possibly a big part of your problem. You "went along" at a point at which it might have been better to "take charge". This led to a number of your other dissatisfactions, I think. But you can take charge without making a clean break at this point until you see something that you really want to do.

Also, since you were chosen you should have confidence that your skills are not in doubt.


Is it ok to write back when no response has been received from a postdoc application?

During academic job applications, I did not hear back at all from at least two places (in the UK), so I would not assume you will hear back. On the other hand, there was also the situation where I had not heard back from one of my top choices so I contacted them and they told me that someone was supposed to have contacted me two weeks earlier but somehow didn't. It wasn't good news, but I had been stalling on agreeing to another position so ultimately it was helpful to just ask, politely obviously. I really don't think it would hurt your situation, and as others have mentioned, may even help it.


Can one get a second Master's degree in a related field (biochemistry, bioinformatics)?

Broadly, yes.

Previously, I worked with students on masters degree who already had other masters degree or other postgraduate qualifications.  Some even had doctorate.  Taking a second masters can be really valuable, especially if you are seeking professional development.

It would depending on the institution that you are applying to for your second masters (such as how you meet the entry requirements etc.), so you would need to check with them for advice on your specific situation.

There are two considerations you need to make, however (this is speaking from a UK context):

Funding

Some funding, especially in the UK, whether student loans, scholarships from private donors, government money and research grants will not cover someone who is taking a qualification of the equivalent level that they have already obtained.  Check this with the university you are applying for.

Visa and immigration

I am not qualified to give visa advice, however, you should know that, at least in the UK at the moment, the decision to grant you a student visa might also depend upon whether you are taking a qualification equivalent to the level of one you have already obtained.

If you're an international student and got your first masters in the UK, your chances of getting a visa to stay to do a second masters could be nil.  Speak with a visa and immigration adviser at the institution you are thinking about.


How are interdisciplinary degrees viewed by disciplinary (AACSB) faculty hiring committees?

When a department looks to hire, they have to make an official statement about which degrees should apply to the position. So the first place to look is job ads for positions you are interested in. There should be a sentence like, "Applicants should have a Ph.D. in ..." to show the "acceptable" degrees. As Business schools typically hire in the Fall, there should be many examples of these job ads currently circulating.

However, what departments do is more important than what they say. Notably, departments may say they are open to interdisciplinary degrees, but then only hire from disciplinary programs. To check this, you should look at the CVs of current faculty at AACSB schools who have HR focus and see what their qualifications are. Especially look at newer faculty hires. If some substantial portion of current faculty come from interdisciplinary degrees like the one you are considering, then I think you would be in good shape. Otherwise, I would reconsider your plan.


Are datasets really random for Bioinformatics tools

What you are describing here is an in silico form of Cherry Picking Fallacy. Before answering your questions specifically, I would like to point out that before assuming bad intent or foul play, consider the biological variability in the datasets, and difficulties writing generalised solutions to biological problems. Take it from a 3rd year grad student and a bioinformatician in training, it's not straight-forward to develop tools for biological datasets. There are both biological and technical challenges in writing "foolproof" software in bioinformatics.

Consider for instance, that there are multiple ways to estimate error and false discovery rate (FDR). There are also varying levels of thresholds used in different labs. Any heuristic value, if hardcoded, might alter the results.

Similarly the biological diversity, as well as technical variability introduced by wetlab benchwork will likely have serious influence on the datasets. Once everything boils down to a large table of numbers, all of that variability is implicit and thus often forgotten.

That said, my answers to your question(s):

No it's not common to pick datasets just to show that your model/software works, at least not publicly. That would go against scientific rigour and ethics. At the same time, you start from what you have available. I typically start with datasets we have in the lab, when I start developing a new tool. But in order to publish your method, you should typically show that it works on data from independent sources, or alternative data types etc. All in all, your results might not be representative of all datasets out there.
It is impossible to answer this question, factually. I am sure there are reviewers that take a look at raw data and/or source code, but it's unlikely that any reviewer actually digs into the source code, line by line, to see if everything checks out. But I am also certain that there are some who just see if you have actually made the source code or test datasets available or not, without actually look at them.
You can always do that, end-user or not. But beware, before you go blowing the whistle on someone else's handiwork (which probably took them a significant amount of time and money) you better get your facts straight. Claiming that they are selling false results or simply misinterpreted their results is a very serious accusation, especially if the authors are renown and respected in the field.

Prior to writing a letter to the editor (who AFAIK have a duty of publishing scrutinising critique on something that has been published in that journal) you should check, and double check, your results. Make sure you are not misunderstanding the statements made in the original work. Make sure you are not misunderstanding your own results. Make sure what you have observed is not a side-effect of your datasets or your own use of the software, try to talk to other people who have used the software. And make sure, your supervisor (and others in the group) are behind you, get your own results investigated by your superiors and colleagues.

If everything checks out you can, and should, inform the journal that the results in the original article might not reflect a general reality, and that you could not replicate the results on independent datasets, then show your results.


Can I include new experiment results in a Camera Ready submission?

No, this would usually not be allowed. One important aspect has not been explicitly covered in Buffy's answer: bypassing peer-review.
Adding new experimental results can significantly alter the paper's contributions and conclusions, and adding them while submitting the camera-ready version bypasses the peer-review process. This is also the reason why many conferences that allow rebuttals to reviews do not allow adding new results even in the rebuttal. For example, the guidelines of CVPR 2021 state:

The author rebuttal is optional and is meant to provide you with an
opportunity to rebut factual errors or to supply additional
information requested by the reviewers. It is NOT intended to add new
contributions (theorems, algorithms, experiments) that were absent in
the original submission and NOT specifically requested by the
reviewers. You may optionally add a figure, graph or proof to your
rebuttal to better illustrate your answer to the reviewers' comments.


Using other college/universities notes for practice?

If they've put it up freely available online, then they have made it available for people like yourself to read. Enjoy!


How do grad schools view early High School graduation?

Graduate schools do not generally care about an applicant's high school record, unless the applicant has some exceptional achievement from high school. Applications to graduate school won't even require high school transcripts.

In particular, graduate schools generally do not care at all about non-academic extra-curricular activites, whether in high school or afterwards. See this question for more details.


Every university is different. However, my university (UT Austin) has, roughly, three research-only track positions: Research Associate, Research Scientist, and Research Professor. None of them are tenure-track or require teaching, and they all are roughly equivalent to the tenure-track positions: Assistant Professor, Associate Professor, Professor. Research Scientist has roughly the same promotion requirements as Associate Professor but only requires 3 outside letters rather than 8, and is a little lighter than the research and service requirements to the best of my knowledge. Both tracks can be proceeded by a postdoc position, but often do not. I started at UT as a Research Associate straight out of my PhD program and was later promoted to Research Scientist.

These positions are offered to give the university a place for professional researchers in non-teaching roles to work without the constraints or requirements of a teaching job. We have lots of them only mostly grant/soft money at the computing center where I work.


I don't think this is a bot. It looks more like a (somewhat misguided) real human, who may or may not be operating under a pseudonym. Based on what I think is their LinkedIn profile they seem to be a reasonably well-educated person with extensive experience working for IBM (or so they claim), so not your average crank. That said, their contributions to vixra seem fairly cranky to me, especially since said contributions mostly consist of extensive compilations of existing material, without a lot in terms of attribution.

Note that there is also a website apparently written by a "Rich Norman" praising George as "a mouthpiece of the possible". Rich Norman claims to be an "artist" of some sort, who has also written some books published by "Standing Dead Publications" (owned by Rich Norman). The over-the-top praise, strangely flowery language, and the unstructured list of what appears to be pretty much the entirety of Georges work makes me think that there is a connection of some sort between George and Rich. Maybe they are the same person, but it may also be a case of a fringe artist being intellectually attracted to a fringe scientist.


In which section of a research paper is it best to justify the choice of methods?

Methodology section should focus on your own method (or algorithms or mathematical modeling) for the research.

Alternative approaches should also be discussed there in the same section precisely (if the alternatives are not highly different from the principal trunk).
The pros/cons of your approaches should be discussed in "Results and Discussion" or in the "Conclusion" section with points.
Why you selected the approach belongs to "Introduction" along with a small statement in "Methodology" itself.

Overall, methodology section tells the story of "HOW" rather than too much of "WHY". "WHY" should belong to introduction.


What is the proper way to include a link to a web archiving site in a list of references?

You could write

  Beard, M. (2003). Non-terrestrial channels overtake BBC1 and ITV1 in ratings for first time. The Independent. [online] Available at: http://www.independent.co.uk/news/media/non-terrestrial-channels-overtake-bbc1-and-itv1-in-ratings-for-first-time-116550.html [Accessed 18 May 2017]. (Archived at https://perma.cc/9TR9-WBRG.)

Or, you could use an archive site that includes the original URL, e.g.,

  Beard, M. (2003). Non-terrestrial channels overtake BBC1 and ITV1 in ratings for first time. The Independent. [online] Available at: https://web.archive.org/web/*/http://www.independent.co.uk/news/media/non-terrestrial-channels-overtake-bbc1-and-itv1-in-ratings-for-first-time-116550.html [Accessed 18 May 2017].

I favour this instance, because you only need to include one URL. (The original URL is clear from the archived URL.)


What can a student in England do, if her Disability Office refuses PDF versions of textbooks?

I have an alternative take on the circumstances.

From Wikipedia, a Print disability refers to an impediment that prevents the reading of printed material. Presumably, the PDFs the disability office has are intended for students that need to use some other method, for example: 1) a text-to-speech program, which can't operate on the printed books, or 2) a digital display for a student with a disability that prevents them from turning pages.

It sounds like your sister has trouble carrying physically demanding loads, like a heavy textbook, but that doesn't mean she can't read a textbook that is sitting in front of her on a table. If this is correct, indeed your sister may not meet the definition of "print disability" that the DO is using.

Although the publisher sent your sister to the DO to obtain PDFs, they probably want no part in assessing whether the accommodations are necessary, they are punting it to the DO. The DO, on the other hand, might have a specific licensing agreement with the publisher that only allows them to provide digital copies if certain criteria are met under their definition of "print disability." It is possible that difficulty with the weight of a textbook doesn't fall under their terms.

I would suggest meeting again with the DO before escalating this to other offices, explain the nature of the disability, and see what accommodations can be made. Personally, when I was an undergraduate student carrying around heavy textbooks just wasn't a good idea for anybody. They were rarely actually needed in a course, they were used at home. It might be that the DO would rather provide a physical textbook copy in courses where a physical copy is needed in-class on a course-by-course basis, rather than providing PDFs (which they may not have a legal right to distribute).

Alternatively, as others have suggested, your sister could obtain digital copies on her own if possible.

(just to add: I think it's unfortunate, to say the least, that the DO didn't directly suggest other accommodations. You have a right to be frustrated by that, but I would try to be polite in the short term and try to assume that the DO head is simply busy rather than negligent. DO's could very easily be understaffed. Maybe they truly are just a jerk, but if they aren't and you assume they are, it will make the situation more difficult for everyone. Assume the best, try to be proactive, try to be assertive without being demanding, etc.)


Do I need to ask permission to provide a narrative of a scholar's methods?

For writing a narrative about published research in your own words, you need a citation and that's it.
For quoting directly from short passages of published research, you need a citation and indication that this is a direct quote.
For images/figures you likely need permission from the publisher unless the images/figures have been released with a license that allows you to reuse them (you'll have to check for each individual image) or if your use falls under some form of "fair use" (the term is used in at least US and UK copyright rules; similar doctrine may be present in other countries). Writing a textbook you intend to distribute/sell is probably not fair use. Putting the figures in a slide show for educational purposes of your own class probably is.
If you were writing an entire book about one (living) subject I think it would certainly be good manners and perhaps a useful collaboration if you were to contact them and get their blessing, but it would not be strictly necessary to do so. It sounds like your intent is instead to provide narrative research descriptions from many different scientists at an appropriate reading level for your target audience, so I don't think it's nearly as important but you might still find some benefit to reaching out to some - scientists are typically excited to share their work, especially if it's an opportunity to spread their research area to the next generation.
Lastly, I'd urge a bit of caution in your approach. Papers these days are typically written in ways that suggest that science is clean and linear, when in fact it is often messy and circuitous. Your approach seems to make it even cleaner and more linear. It's common for textbooks to take this simplified approach to historical experiments, but it doesn't necessarily convey what science really is to people who may be interested in pursuing it. The conflict in expectations can be quite distressing when it is first encountered.


Scopus and Web of Science give different h-index: who should I trust?

Both (and neither).

Like other citation metrics, the h-index compiled by these databases only depend on what's already in those databases. Both of them have quality barriers, which means you could well have been cited somewhere else but neither of these indexed it. That's why your Web of Science h-index is almost certainly going to be lower than your Google Scholar h-index. In the same way I'd guess that your Web of Science h-index is lower than your Scopus one.

In other words, your h-index depends on what database is used to generate it. You could say your h-index is 15 and it wouldn't carry meaning; you need to say your h-index is 15 as measured by Web of Science.

I'm not sure how seriously the job you describe treats the h-index. If given the option, I'd report both of them (and the one by Google Scholar). Otherwise just give the higher number, and expect to defend it in the interview.


Active voice: Using "I" to show my contribution and "we" to include the audience?

Apart from issues of singular versus plural first-person in active voice, ... it is often possible to use third-person (active), simultaneously shorten the sentence, and perhaps only refer to the objects, phenomena, and processes in play. E.g "Application of procedure X to stuff Y produced whatever-Z..." (Or "Procedure X applied to stuff Y ...")
That is, often, "unwinding" the grammar can show that there are redundant or functionless phrases, which can be dropped, and in fact clarify.
(In my field, mathematics, in English, in the U.S., there certainly is a tradition to use plural first person, but, truly, I've found that often unwinding the grammar allows shortening. And, often, unwinding allows active voice rather than passive, and shortens and simplifies.)