How to analyse the following reviewer comments?

These are all fairly clear.

  There are missing references to recent literature, which are closely
  related to this submitted work.

Exactly what it says on the tin. The reviewer believes you are missing references, and importantly, recent references in areas close to what your paper is on. You should find them, and include them. More importantly...

  A proper comparison of results and the methodologies among these
  efforts, as well as clear motivation for the incremental progress is
  typically required.

Your reviewer is asking you to put your paper in research in context with those papers. What does this add? Why did it need to be done. What is the motivation of the work?

  In addition, the submitted paper has several typographical and
  organizational errors.

This, again, means exactly what it says. The reviewer has found what they believe are typographical errors, and errors where the paper isn't well organized - for example, possibly where a section relies on something not yet introduced.

  The decision is "reject".

  Should I resubmit to the same journal after making corrections or to a
  different one?

If they wanted you to revise and resubmit, that would have been the decision. A flat "Reject" decision means you will need a new journal, though I would suggest taking the reviewer's comments to heart. It's possible they're correct, and it's possible you'll get the same reviewer again.

To expand a bit on your comments, because replies are a bad place for nuance:

  I have one question? suppose i sent this paper to a lower standard journal and the same reviewer gets hold of the paper, will his/her review change subject to the journal

This is very unlikely. You might get away with it if the primary criticism was about the novelty or importance of the paper, or not fitting with the right audience. But, to be direct, the reviewer's comments are things that would be fatal flaws in most respectable journals - just going down a tier won't fix them. Instead, I'd strongly suggest you mull over the reviewers comments, go looking for the recent studies they mention, etc.


Do extracurricular research/activities in graduate school negatively affect your future?

Read broadly, publish narrowly deeply.

This is roughly what I've been telling my students. Now all of this depends greatly from area to area, but here's what I believe to be true. Having a broad background in your area might slow you down initially when trying to publish. But over the long term (your entire career), a broad base will help you more - it will let you be flexible about topics of interest, it will allow you to see connections where others might not, and it will help you place your work in a larger context.

But from your question, you appear to be referring not just to "exposure to outside topics" but "activities related to the larger enterprise of science and academia". With those activities also, you should be careful. Maybe choose one or two outside activities and devote your extracurricular efforts there. The advantage is that by focusing, you're more likely to be able to do something meaningful, and it also prevents you from frittering away time in busy work.


Why did SoftwareX’ impact factor drop from 4.5 SJR to 0.4 last year?

I think this is a good example of putting too much faith in an average measure like Impact Factor or SJR when you talk about the 'reputation' of a journal.
In 2015, in its first year, SoftwareX published "Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers", which was extremely highly cited - Scopus has almost 3,800 citations, more than 40 times more than the next most-cited paper in the journal. The journal is quite small, so in 2017 SoftwareX would have had a “citations per paper” of about 8 from that one paper alone.
SJR uses a three-year window, so this paper stopped contributing to their average in 2019, which is where you see the precipitous drop in rank, as it's now reflecting the 'normal' citation rate for other papers in the journal without this huge outlier.
The question you have to answer for yourself when deciding where to submit is, should you care? You said SoftwareX had built a reputation as a respected and leading journal, so if that was actually true in your field, then nothing seems to have changed apart from this one big outlier dropping out of the citation average. On the other hand, if 'reputation' was just used as shorthand for Impact/SJR, then this has indeed substantially fallen, and you'll need to decide how much that matters to you when you decide where to submit.


Is it reasonable for a professor to ask students to stay 30-45 minutes past scheduled class time every week?

I guess I'm going to be the contrary opinion here. I don't think your professor's request is reasonable at all. Class time is scheduled the way it is so that people can plan the rest of their lives around the schedule. In this case, nobody but you seems to have anything from 12:50 on, but that shouldn't encourage the prof to monopolize that time.

Some may think your extracurricular activity is trivial or that you should skip it, but that math club could easily have been another class or your job. The professor is in a position of power, and he should respect his position by not trying to compel you to work outside the system because it's convenient to him. Several of your peers may actually appreciate that you're the lone hold out even if they won't ever admit it.

I would have no problem with the prof offering extra sessions where no required material was covered. This could be extra practice working example problems or a Q&A session to clear up anything confusing from class. That being said, I think professors should be held to teaching the required stuff in the allotted time.


ArXiv was not interested in expanding into biology (apart from quantitative bio). A 2013 Nature news article about the establishment of bioRχiv explains:

  ArXiv’s quantitative biology section, launched in 2003, has seen exponential gains in the past two years [. . .] But arXiv does not plan to expand into other areas of the life sciences, such as cell and molecular biology, and the site is not designed with biologists in mind.

In 2018, arXiv Operations Manager Jim Entwood discussed how the arXiv decides whether to expand into new subjects, saying that they ask "How does the proposed category fit into the rest of arXiv?" and that they are "fairly conservative when it comes to adding new categories".

  This comes in part from our general principles, and our commitment to those communities we already serve. We also need to ensure sustainable growth both in terms of active engagement with research communities and the financial and organizational capacity of arXiv. Decisions for category expansion are ultimately up to the arXiv Program Director and Scientific Director with input from arXiv staff and the Scientific Advisory Board.


There are two issues in my mind. The first is not having the post doc supervisor as a reference. As you get further along in your career, you will have to leave someone that knows you well off your list of references. If you can develop a strong enough network that you have 3-5 people who know you and your work well and are willing to write you strong letter, then the absence of your post doc supervisor will not be seen s odd.

The second issue is more problematic and that is if your post doc advisor is contacted informally, he may actively or inactively sabotage you. In order to get around this, you need to repair the relationship, such that it is not a problem. As a first step, make sure that he is really unwilling to be a reference. If that is the case, then make it clear that you will not use him as a reference. Ask him if he is willing to tactfully deflect informal enquires. If he is, and you believe him, that you do not have much to worry about. If not, consider having one of your letter writers address the issues you have with you post doc supervisor.

Having a reference point out bad things is always dangerous in that it makes the hiring committee aware of something they might not find out about. The advantage is it is the only way to really get your side of the story told. It is worth talking to your other references about how to address the issue.


How to collect data for dissertation if the work wasn't published

Very hard to answer without knowing the details of your work, the app in question, more background, and what other contributions you can make part of your dissertation. But… even if a formal release isn't possible by the deadline, couldn't you arrange for testing on outside people but on your devices (instead of theirs)? That way, you can load the app on a series of say, 10 devices, then have people test it (sort of a focus group)…


I don't think it's worth it. I've seen conference program committees accept papers with such scores many times. I think if you address this reviewer's concerns, perhaps offering some changes in the introductory parts to reemphasize the main result, you've got a better chance of acceptance than if you ask for special treatment.


Student feedback and jealousy between colleagues

My feeling is that most colleagues just don't care about the feedback. Long before those feedbacks generalized, we already knew who are the good and bad teachers. However, when I was in charge of one year of our engineering program, I tried to move teachers from the lectures where they were poorly graded. It's not easy, but it's do-able. Luckily, it seems uncommon to be globally bad at teaching, so I was always able to find a place for everyone.


In the US, a "research assistant" is typically a graduate student, or occasionally an undergraduate. A "fellow" is somebody funded by a scholarship - it indicates you aren't being funded because of the merits of your research project but primarily because of your personal merits as a scholar. Sometimes "fellows" are also more senior positions (senior non-professor PhD roles in academic laboratories, or some PhD researchers outside academia) and there the title implies some additional autonomy beyond other employees.

Research Associate is the title typically given to post docs, but can be more broad than "post doc" which implies a training position. Including the information from your previous post I think it is the title that would be used in a US context that is most equivalent to the position you describe. Note that all of these designations apply mostly to academia: titles in industry can be completely different and vary a lot by field.

My suggestion if you were wanting your CV to be most understandable to someone in the US or familiar with the US system would be to write your title from your contract, untranslated, and in parentheses you could translate it as "Research Associate."


Are there opportunities to support cancer research through volunteer IT or software development?

I greatly admire your interest in contributing to an area of medicine, and I'm sorry to hear that so many of your friends and relatives have succumbed to this disease. You're absolutely right that the treatments are barbaric. The subject of personalized medicine with application to cancer treatment is a hot scientific topic right now, and we're probably on the verge of a revolution in this area.

Two specific groups come to mind as leaders in this though I'm sure there are more. Levi Garraway's lab at Harvard is developing "PHIAL", which stands for "Precision Heuristics for Interpreting the Alteration Landscape" [in cancer genomes]. The name alludes to Galadriel's phial, although it remains to be seen whether this sort of computational analysis will live up to being 'a light to in dark places, when all other lights go out.' It is exactly what you imagined in your post, that is, given DNA sequence, predicting candidate causal mutations. There's also Tim Ley's group at Washington University in St. Louis which was one of the first to sequence a patient (one of their own oncologists!), identify the specific mutation and treat his cancer. The story is pretty compelling, but it's worth noting that this was a fortuitous situation where the underlying mechanism just happened to be one treatable by a drug already on the market.

Laboratories are always underfunded -- your services would be a gift. It's just a matter of finding the right one. If you live in a major city, consider contacting some people in cancer to identify someone in computational biology or bioinformatics. If you post what city you're in, I (or others, I'm sure) could help you find a lab doing this sort of work already. Good luck!


Selecting the Theory Underpinning the Research Project

Whenever you have a problem you can't solve, solve any part of it, then take another look at the problem and see if the partial answer has helped. (I can't find the exact source of this formula, but I think it's R.A. Heinlein.)

First, what sort of methodology are you considering? Interviews? Surveys? Online or in person? What sort of statistics are you contemplating, if any? How will you assure you have something representative rather than the result of a small number of people with unusual opinions? How will you select your subjects? Is there any method to deal with self-selection? For example, people who are unusually happy or unusually unhappy are possibly more likely to want to talk about their experiences.

You write of differences. How will you determine the situation before they migrated in order to observe the difference? Suppose, for example, that you had a significant number of people with very little work experience outside of Australia, maybe because they migrated in the age range of 10 to 18, and so didn't have jobs previously. How would you discern "coming of age" factors from "changing culture" factors? Possibly you need to do some research on the situation in the places the migrants migrated from. Possibly you need to compare to the perception of experiences of non-migrants in the same age range. Possibly you need to control for financial status, education status, etc.

How will you detect the just so story in your work? If you do detect it, what will you do about it?

There are a bunch more such questions you could ask yourself. I'm a humble safety analyst, so I know very little about sociological studies. I do know something about how to avoid fooling yourself.

Once you have some notion of that, then you can look at theories that you could possibly test using such methods. Then you can refine your methods to target specific hypotheses. Be sure that the research you propose has a reasonable expectation of actually testing your hypotheses. Also, have some thought as to whether there might be alternate hypotheses that have similar explanatory power.

And after you've done all that then stand back and critically examine the whole thing. Maybe there are other methods that would be a similar amount of work (or even less work), but that would test these hypotheses more accurately. Maybe there is already a block of research that tests them. Maybe there is some reason to think some of your hypotheses are wildly wrong before you even start.


When a journal requires that the work has not been published before except as a "preprint", is an arXiv publication considered a preprint?

Usually depositing a paper in arXiv prior to journal submission does count as a preprint. Wikipedia explicitly says so...here's the wiki link: https://en.wikipedia.org/wiki/ArXiv.

You can check out this list of journals with preprint policy: https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy
If you posted your paper in arXiv before submitting to the journal, do inform the journal (include the link to your paper in arXiv). From your post, it seems that your journal does not have such a tight preprint policy.


How can a student suggest changes in grading policies

Once published, I don't see any easy way to change the grading scheme for a course "in progress."

However, if you mean to suggest how he can more appropriately grade assignments and examinations, that's a different matter. The best way to do this would be to start the conversation with a polite inquiry into why certain decisions were made.

  I'm a little bit confused about how this assignment was graded. You told us we should do X, but you did Y instead. Is Y something we should be doing instead of or in addition to X?

This initiates a conversation, rather than looking like an attack or direct criticism. It's usually a more effective strategy for achieving results, particularly when face-to-face conversation isn't possible.


Expelled from undergrad university for poor academic performance, can I go back there (years later) for Masters?

Keep trying!  I was on academic probation (at a Canadian university :-) ) after my first year of undergrad (2.88 gpa). Thankfully I did not get kicked out. I persevered and now have an MSc and PhD and have been doing medical research for many years. Don't take this as gloating, just trying to say anything is possible :-).

Now, it will depend a lot on the university or department, but if you can convince a faculty member in the department that you want to do research and that you have completely changed your attitude, maybe they will have some sway (at least with the department).  In my field, it is primarily a matter of convincing a faculty member (assuming the grades in the "lesser" university were good).  Again, this will depend on the department.

Alternatively, maybe you can make an appointment with the admissions department and make a case to them why you should be allowed back in to the university.  I suspect many would take your 7 years of experience as a growth experience.

Good luck!


Is there a tool for showing trend in a technical research field?

I use Scopus quite a lot and it provides the ability to analyze keywords (there is a link to 'Analyze search results'):

I was able to quickly obtain this plot for publications per year for the keyword 'wearable computing':

It can also be restricted to particular sources. For example
this one for 'wearable computing' in 'IEEE Pervasive computing':

Unfortunately you need a subscription to access Scopus.


Letter of recommendation from online classes

Assuming these are proper online courses, with proper work you turn in or at least exams, you should just email a couple of professors a month or 2 before you need the letters.  Explain the situation, briefly remind them who you are, and ask for recommendations.
They will be able to say in their letters what was covered in the course and evaluate your performance, so choose professors who you think will be most familiar with your work.

This shouldn't be that different from a letter a professor for a class you physically attended, but who you never had much personal interaction with.  Note you probably get at least one reference from your undergraduate days, at least assuming that was reasonably recent.


Preparing a manuscript for double-blind review, what is meant by "complete manuscript text minus the title page" and "separate title page"?

The basic answer here is to ask an editor since it's your first submission, but I would think that this sounds good. There's a lot more to preparation for double-blind review than taking your names off the front. You've got to do a good job making your self-citations look like references to other people. I.e., instead of saying "in [5] we showed" you say "in [5] Layal, et al. showed", etc, etc.


Justification statement for exceeding the maximum length of manuscript

Assuming it is true, I'd say that I'd made a good faith effort to keep it to the limits, considering whether any of the material was extraneous, but it is still at 37 pages.
But also add that you would welcome advice from reviewers including advice on reducing the length.
I doubt that a detailed technical statement will get the result you want, since the editor may not be able to evaluate what you say since that is more the job of reviewers.
Some papers can also be split into two, of course. Perhaps you have considered that already. Not all, of course, but it is worth a look.


Saying no to student requests for excessive appointments and help solving homework

I would limit the amount of time you dedicate to a single student to a maximum of 20 minutes a week. This is a reasonable amount of time to discuss the main problems a student has. This does not mean that you cannot make exceptions, but it is good to have a general rule.

As a side remark: You will not make everybody happy. If somebody wants an appointment and you say "no", and he insists, you can still say "no" and walk away.


Can you do a post graduate in Math(or some other hard sciences) if you major in a soft science?

I think what you know and how strong your recommendation letters are the most important factors during the application process. Usually people need to take several foundamental courses to have a solid background before conducting research in math. And you also need to have some undergraduate research experience. So a degree in math is the most efficient way to get this. But it can also be achieved even though you don't have a degree in math. My undergraduate degree is business administration but I have taken around 20 math courses including 10 analysis courses and several algebra and geometry courses during my undergraduate study. Currently I am going to start a research master program in pde and applied analysis and I hope I can do research in math in the future.

So yes, you can. But you need to make extra effort to fill up the gaps.


What to do in the summer if math REUs reject me? Should I still apply to grad school?

REUs are a nice way to start to get a sense of what mathematics research is about, and can certainly be helpful for graduate admissions.  But they're not a prerequisite.  You don't need to give up on grad school just because you didn't get accepted to an REU.

As for what to do with the summer, if you are interested in research, consider trying to work on a research project with one of the professors at your university.  You say you want to do this next year, so it would be even better to start this summer, when you will have more time available and won't be distracted by coursework.  Start asking them about it now.

I think it is definitely a good idea to have some sort of research experience before applying to grad school.  Partly because it is helpful in admissions, but mostly because it will help you decide if it is actually something you want to do.  Mathematics research is a very different experience than coursework, and before committing to doing it for several years, it would be wise to see if you like it.


Who decides whether to accept a paper: reviewers or the editor?

Accepting or rejecting a paper is always left to the editor.  The reviewers, however, are typically expected to summarize their review by providing a recommendation to the editor for the paper's fate.  This is generally not just accept or reject, but may also have higher granularity such as "major revision," "weak accept," "reject but encourage resubmission," or "borderline."

As an editor or program chair, I appreciate this feedback (even if I may sometimes ignore it) because sometimes it is sometimes difficult to judge a referee's judgement from the tone of their review.  For example, a very long and harsh-sounding review may actually say something like: "I am being very strict in my review of this paper because I think it is good work that can be a great paper on revision." I might overlook it amidst the harshness... or the reviewer might not be so clear.


What are the pros and cons of laptops in a classroom?

I think due to increasing lecture sizes, and in complex or technical courses, having something like a tablet or laptop is considerably useful!

There's something to be said of classroom etiquette, however, in that not everyone is equally courteous. Some big no-no's for most of my lecturers were:

(1) No recording via the built-in camera, especially without permission, and no holding things up and taking photos. People learn in different ways, but we have to standardize the classroom somewhat, because not everyone can idly sit by and concentrate while 10-20 people are holding up their tablets, taking flash photos, or doing something otherwise weird/distracting to copy lecture notes.

(2) If you have the slides up on your personal device, make sure it's the only thing you have up unless otherwise specified. No one wants to see someone elses Youtube, Facebook, etc. during the lecture.

Beyond that it is distracting to hear the tapping of many keyboards vigorously trying to take notes all-at-once. I think that these people do themselves a disservice by taking word processor notes, however, and that to a great extent hand-writing the notes even if you have a personal device helps to enrich you in the material. My personal method was laptop set to slides, write notes on paper. But again, not everyone learns the same way. At that, for some complex courses I constantly search terms I didn't understand or concepts I might have forgotten about so I don't get utterly lost in the process. To me this decreases the amount of hand-raising and review questions.

I think that having some ground rules, and a little talk about common courtesy in the beginning of the term is good. It's penalty enough for some people to get called out for being discourteous in front of the class, so a ban? Perhaps not. And like I said in the beginning, lecture sizes are up there and not everyone has choice hearing/vision, so laptops/tablets help supplement those people who can't see the presentation or can't hear the lecturer.


Is attending (and presenting at) a summit taken as an "honor'' in a CV elevating the chance for tenure-track applications?

I think this strongly depends on the field.

In pure mathematics, I think nobody would be the slightest impressed by "represented my university in the future research leader summit, which managed to heap 25 nobel laureates into a big pile". It might even have a slightly silly and vain vibe (whereas everyone would be ecstatic about an invited talk at the ICM).

But this could be completely different in other fields; so I think your best guess is to trust the opinions and reactions of the (senior) colleagues in your field.


Publish a Book Through a Research-Based or Industrial-Based Publisher?

Both are valid aims:

Academics are paid for doing academic research, that is our job.
Academics are often (partially) paid for by tax money, so it is perfectly legitimate to communicate what you did with that money back to the general public.

There is usually some specialization: Some academics are good researchers but awful comunicators, so they won't write books for the general public and that is a good thing. Even those academics that are good comunicators will also publish more narrow academic works: the point of communicating with the general public is to communicate what scientific work you have done, so some scientific work needs to preceed the work aimed at the general public. Finally, it also depends on the state of your carreer: If you don't have tenure yet, I would choose to focus on projects that increase my academic reputation. When you have tenure you can afford to make more balanced decisions.


May I include results from a collaboration in my PhD thesis?

I had a similar situation in my thesis, in math. The third chapter was based on a work that was jointly done with another researcher, a professor from another university. (In the end the paper we published was even with two other researchers, as we decided to join our efforts.)

I had to ask the researcher for permission to include our joint results. This is a no-brainer (though of course he was happy to let me do it). When I sent out the thesis to my committee (of which he was part), I also sent him a copy beforehand and asked him if he was okay with what I had written, as they were his results too and he might want to check that I didn't mangle them before releasing them into the wild. My advisor also was on board from the start, but I imagine that you have to ask for permission if this isn't the case.
I had to include acknowledgments for this in my thesis. Basically, I wrote a paragraph at the beginning of the chapter, stating "this chapter is based on joint work with [...]". Again, this is a no-brainer. I cannot claim all the results are due to me if they aren't. However, I didn't say anything of the sort "I did X% of the work and the other researcher did (100-X)% of the work", this isn't how it works, and it would have been in rather poor taste. At least in mathematics, it's expected that co-authors contribute roughly the same amount of work to a joint paper, but it's not an exact "50-50" (or 33-33-33, or 25-25-25-25...) distribution.
The whole thesis had to be written by me, in my own words, including the results and the proofs that were actually due to the other professor. Moreover, I obviously had to perfectly understand, and be able to explain, and defend, all the results, as if they were mine.

All of this was explained to me by my advisor. It's possible that regulations in your university say something different. The essential part, I believe, which is only hinted at in the steps above, is to ask your advisor what to do exactly.


This really depends on the graduate department.

At a minimum, however, you should not expect to come up "short" on funding because you brought in an external fellowship. Someone should offer up additional money to bring your total package up to the standard level given to your colleagues in your department. Whether or not the funds come from your supervisor or from the department is for them to decide.

The exact mechanism also varies by department. For instance, in the departments I applied to as a graduate student, one gave a sizable bonus for bringing in an external fellowship (an extra $8,000 per year), while others "topped off" the stipend up to 110% of the stipend of students' normal stipend.


How to learn commenting on graphs and tables the right way?

One problem people often have when presenting data in graphs and tables is that they often include data that is not relevant. For talks (formal or informal) I really like the process of starting with an empty graph of just the axes and explaining what the axes are and the limits and what they mean. Sometimes I then like to show idealized data from competing hypotheses so people can know what to expect without the added difficulties associated with understanding real, and potentially noisy, data.

Once people understand what the axes mean, I add data to the plot. Ideally, I start with a single data point and explain exactly what the data point means. I then add additional data points from the same "condition", possibly one at a time if they are discrete or all at once if there is some meaningful function that describes them. Once the first set of data is presented, I add on the second set. Sometimes it is helpful to remove or grey out the first set of data while you are introducing the second set of data so people can focus on just what is new. Once the second set of data is explained, bring back the first set and talk about the relationship between the two sets. This should ideally be moved to a new figure or panel to highlight the differences and similarities you want the listener to focus on.

If there is more "hidden" in figures and tables, that means it is too complicated for a talk. In manuscripts space is at a premium and you often have to have figures that tell multiple stories. In these cases the text still needs to walk you through the figure step-by-step and introduce each piece of information in the order in which you want the reader to look at it.


Link which explains how to format a letter to Nature

Such information is invariably posted on a journal's website, and Nature is no exception. Go to Nature's current issue website, click "For Authors" and "Manuscript Formatting Guide". Under "Letters" there is an "annotated example" which looks like what you are describing.


Is it normal to submit an abstract to a conference when the research
  is NOT completed?

Sure.  There are plenty of fields where the purpose of a conference is to discuss research that is "still cooking."  In fact, many journal publications can be viewed as interim reports on larger research programs that are still in progress.

You might use this opportunity to set a goal for (roughly) the piece of your thesis you want to have done by the date of the conference.  It's ok if that piece is relatively small, and nobody at the conference will hold you strictly to what you say in the abstract.

In fact, some people submit abstracts on one thing and then talk about something entirely different... I won't advocate that behavior as an intentional strategy, but I will say that many people (myself included) prefer a great talk to exacting consistency with the abstract.


How should someone choose a PhD topic so that she doesn't fail?

Make sure your advisor has a good track record of graduating students in time.
Anyone just entering or outside the field won't be able to assess PhD topics with good judgement, so it's unfair when advisors fail their students by giving them bad projects. Your best bet at avoiding this is finding an advisor who is unlikely to fail students in this way.
If you find yourself in this position, a good bet is to reach out to other professors and tell them what's going on. It can feel shameful, but I've seen many success stories of people getting a new project and spinning it into enough for a PhD when things aren't working out with their initial advisor.


Is it ethical/legal to obtain journal articles from reddit?

Legally, I am not sure --- it depends on the laws on the country as well. Ethically, I don't see anything wrong about it. Academia is about building and sharing knowledge: if anything, I would consider it unethical to put papers behind a paywall.


How to mention an implementation tool in thesis?

It somewhat depends of the publication style that you use for your thesis. For example, APA (6th edition) does not recommend to cite standard office software and programming languages.

Therefore, if you would follow the APA guidelines, you'd just mention Python everywhere you need without citing any sources, however, you'd have to cite the MATLAB software. See the "Computer Software/Downloaded Software" section in APA Style Guide on electronic sources for an example of how to format software references. Applying this style, I came up with the following citation (note it's a hybrid of the two approaches, due to my attempt to accommodate the company's geography):

  MATLAB. (2012). MATLAB (Version 8.0) and Statistics Toolbox (Version
  8.1) [Software]. Natick, MA: The MathWorks, Inc. Available from http://www.mathworks.com/products/matlab

Please note that citing MATLAB, following some other publication styles, such as Chicago, is discussed in this blog post. If you use LaTeX to create your thesis, this blog post can help.


I lived through this same situation myself: I had only really known the US system when I accepted a MCF position in France, and was pretty overwhelmed during my first years. For example, my first year I had to prepare several cours magistraux, and I didn't know enough to refuse. At one point I explored returning to the US, in fact for two years I moved back to Boston, but in the end I found a better return on investment making the French system work for me.

Here are some take-aways.

If you are ambitious and your research record is good then you should very seriously consider applying for a position as research scientist at a national institute: CNRS, INRA, Inria, Inserm provide working conditions superior to the best research universities. You can still teach undergraduates if you want to. In my case I went MCF to DR, but MCF to CR is more typical.
Faculty in the US have a lot of administrative responsibilities and committee work that aren't counted towards their teaching load. In most French schools you will get a décharge from your service for this work and you can negotiate that. In the end of my time as an MCF some 40% of my service de 192 was counted this way.
Taking on Masters students early is important for getting ahead, and while the hours counted towards your service don't completely represent the work that is involved, they can be far more rewarding. Especially if you have ambitions.
As a tenured French civil servant you are free from the precariousness that junior faculty face in the US.
In France, advancement is almost entirely based on research output; taking on administrative responsibilities is a necessary evil but will not in itself get you promoted. Don't get suckered into responsibilities early; do enough to show you are a team player but try to save your non-teaching time for research projects.
The US research system is very individualistic, in my experience junior and senior faculty are pretty much expected to go it alone, and hire students to work with. The French system is very team oriented and perhaps half of a team's members will be permanent faculty or staff. Find a good team.


Should the listings be included in the contents page

I don't know that there is a "normal" order over different fields (or even within a field). My only suggestion is that if you need to symbols to understand the listing, then maybe symbols should come first.

Otherwise, what you have should be fine. But for a thesis, let your advisor give you the best advice.


Regarding “given that his name was not added as co-author before acceptance”: ask him ASAP. Be honest, be apologetic, explain clearly the situation and the reasons you did not want to add his name beforehand, but also be very clear that you realize now it was a mistake not to discuss it at the time, and that you made the mistake due to your lack of experience in academic publishing.


Permission on reproduction of data extracted from a figure

I plot the raw data together with mine

The plot is yours, the data is theirs.

  If I publish this plot and properly cite their paper, do I need to ask them for permission?

No, the citation (and suitable explanation) suffices to attribute the data source. Indeed, as noted by the referenced source (under the heading Reuse of graphs/tables...):

...reuse of raw data does not generally need permission, provided you have plotted
it into a different graph/table. You should however cite the source of the data.


Academic Amnesty-vs-Transferring: how does each affect graduate school admission?

Whatever you do, it's worth keeping in mind that those reading through grad school applications are people as well. They understand that whatever happened 20 years ago will not be who you are today. So, if you have good grades in your most recent courses, and if you have good GRE scores, then they will be quite likely to disregard your grades from the last century. Just point out in your application essay that you have had a few hard years back in the day but that, as can be seen from your most recent transcripts, you have changed and gotten yourself back on track. Honesty pays in this regard, and whatever your GPA will be does, in that case, not matter all that much any more.


Why don't mathematics professors use social media to promote their work?

[It's hard to imagine an answer that isn't somewhat speculative, so let me give a somewhat speculative one.  A lot of what I will say is more or less the same as various commenters already said.]

For context, I am a pure mathematician working in the UK, but I did postdocs in the US and in Europe. Here are some reasons I can think of that a mathematician would not use social media to promote themselves in the way you describe.

First, motivation. It takes a lot of work (as well as good fortune) to become a mathematics professor. It's safe to assume that almost everyone who achieves this goal actually wants to be where they are. (Initially, at least.) If we all wanted to work in the tech industry, we would have made a different choice at some point in the past. But we want to do math, and teach math.

The contrast with computer scientists should be clear: it's plausible to think that a computer scientist could move from academia to the tech industry without changing their research focus too much, and then come back to academia if they change their mind. For most mathematicians, though, this move would mean no longer being a mathematician, and most of us don't want to do that.

Second, nobody is going to poach you! (Probably.) This has already been well-covered in the comments, but it's worth repeating. The idea of a mathematician being poached by a tech company on the strength of their research is not very realistic in most cases.

Despite what we write in grant proposals, a lot of the research done by academic mathematicians does not have much relevance for the "real world" outside math. (Even in what is usually called "applied math", my personal impression is that many people are more interested in the research itself than in possible applications.) Of course there are exceptions, but even among these, many people are working in fields not relevant to the tech companies that you describe as doing the poaching.  Other industries may have use for the outcomes of mathematical research, but not the resources to employ dedicated mathematical researchers.

In particular, the scenario you describe of "mak[ing] a few million dollars for a couple years of work - and then return[ing] to academia" is wildly unrealistic for, I would say, the vast majority of mathematicians. To me your second question feels a bit like asking "Why don't more mathematicians spend more money playing the lottery? Don't they want the chance to win millions of dollars?"

Again, by contrast, it seems very plausible that an academic computer scientist might be working on something that is of immediate relevance for a large tech company, so poaching is a realistic prospect here.

Finally, mathematical culture. OK, but even if being poached is not a realistic goal, or not even desirable, why don't mathematicians promote themselves more on Facebook, Twitter, and the like? Don't they at least want to boost their profile and get a bit more recognition? I think the answer to this involves, more than any philosophical reason as you suggest, the norms of mathematical culture. (To repeat, I 'm a pure mathematician, so my point of view is heavily slanted towards this part of the discipline.)

In my experience, mathematicians as a community tend to be extremely sceptical of anything they regard as boasting or exaggeration of one's achievements. The norms of our culture teach us that self-deprecation and understatement are the appropriate attitudes to adopt, at least in public. (Real example: a seminar speaker writes his big theorem on the board, then says to the audience apologetically "Now, this is not entirely trivial...") In this context, using social media to "promote" your work might have the opposite of the intended effect. Instead of people reading, and respecting, your work more, people might start to think of you dismissively as "that Twitter guy".


In CS, conferences are like journals in other fields: the normal medium to publish fresh results. But it is results. There might be exceptions for some specialized conferences that make exceptions.
Also, many CS conferences have a Workshop track in which unfinished work can be presented and discussed. Likewise, there is sometimes a Doctoral workshop in which PhD students discuss their ongoing research and get feedback.
But for a normal paper track in a typical conference, a completed work will be expected.


Is it a misuse of school resources to use school accounts for non-school work?

In the US and some other places there will be laws (at the State level) and regulations about use of resources in general, but for the things you suggest there should be no issues.
But this is because the libraries, in particular, at universities serve as a general public resource of information. You could probably get the same services even if not enrolled just by asking for assistance.
There might be exceptions, but for most universities the mission is varied and broad. A university is more than just a place where students are taught and more than just a place where research is done.
As long as nothing you do actually interferes with any of the missions (and sometimes even if you do), the resources are open to you and, it is citizen taxes that support much of it in any case.
Feel free.

The cases where you might run afoul of regulations would more likely be in the use of specific equipment purchased for one thing but used for something else.


What happens when you terminate a UK Ph.D. in the second year?

The situation here varies wildly depending on your particular program, which is strongly determined by your particular university, which in turn is strongly influenced by country.  Some places will allow it after two years; others have a specific non-time-based criteria (e.g., completion of a Ph.D. proposal or being ABD); others do not allow a Masters exit at all.

In the UK, Ph.D. students are often expected to have a Masters before they even start, so you are definitely not talking about a standard case in that system and need to talk to people at your particular institution to find out the answer.


Should I take an extra but "short" recommendation from a bigshot?

I think he used short as a euphemism for generic. A short letter might still be excellent if it talks about very specific things and is to the point.

If the collaboration was intense during those 2 weeks, he might have useful things to say. More probably though, he warned you politely that his letter would be generic since he doesn't know you well enough.


Why do Universities offer a "Double PhD Program"?

I think the site where you found the information was pretty crystal clear:

  Joint-PhDs are doctorates which are done at two degree-awarding institutions. This type of doctorate, also called split-site PhDs, does not mean that you are simply supervised by one supervisor in one university with another advising you on an informal basis. Joint-PhDs mean that you are fully registered in two universities, having to comply with admission requirements and assessment regulations at both institutions and that it will result either in two PhD degrees (double PhD) or one jointly-awarded PhD (one diploma with the two university logos). The reason universities offering double degrees rather than jointly-awarded degrees is often practical in nature, for example one countrys [sic] legislation does not allow joint-degrees.

I'm not sure which part of this is unclear. Often it's easier for two institutions to each grant a PhD (i.e., double PhD) than it is for them to create a hybrid entity that would grant a singular degree or for the creation of the institutional apparatus and coordination necessary for a joint degree program.


As a TA, Should I allow students to ask their doubts without schedule?

From the student's standpoint it is very helpful to learning to be able to ask questions when they arise, rather than waiting hours or days for the opportunity. But if you are managing a number of students you need to be able to respond to student needs both effectively and efficiently. Also, responding to student questions doesn't always mean actually answering them. More often, actually, you can show them where to get the answers themselves. Their learning will be deeper if they put effort into it, so make them do that. One exception is that you sometimes need to dispel misconceptions that people have so that they don't waste time on unproductive study.

One of the best techniques that I used in the past (I'm retired now) extensively was an email list to which I and all the students were subscribed. I didn't answer questions sent to my normal email - individual questions - but I always saw that student questions directed to the mailing list were answered. But other students were also encouraged to answer questions posted to the list, so that not all answers came from me. I normally had to answer about a third to a half of the questions. Moreover, every student was able to see every question and the answer. Then, you don't have to answer the same question multiple times. And you also have a record of questions that can be useful for future course preparation.

I had to monitor the list, of course, in case incorrect answers were given, and I had to set some ground rules so that answers to exercises weren't given, but generally, the list was very open. People were encouraged to help their classmates learn, by pointing to resources, for example.

Such a list is also helpful if some students are dissatisfied with the course and complain on the list. I never had to "defend" myself on the list but occasionally students would themselves respond to complaints of their peers.

There are, I assume, other ways to do this, but the keys were (a) complete transparency of questions and answers, and (b) ask a question or express a concern at any time, day or night.


If Thomson Reuters says it indexes a journal but it's not mentioned on the journal's web site, who should I trust?

Trust Thomson Reuters, of course. It has all its JCR impact factors up to date.

Beware that there are many journals that print impact factors on their own site with their own definitions making a facade impression to prospective readers and authors. Do not confuse them with JCR impact factors.


Is it legal to include another person's result in my research paper?

Isaac Newton said, "If I have seen further, it is by standing on the shoulders of giants." Research would grind to a halt if each scientist had to start from "scratch."

So the question becomes, "How should I use the work of others?"

The answer: By citing their published work.  Since the number of times a publication has been cited is often used to measure its impact, this is both fair and ethical.


There are two possible issues. If the reviewer simply thinks that units should be provided for stylistic purposes, then you should look through a couple of past articles and see if they provide units. If they do, follow the model. If they don't you can respond with it appears that units are not typically included in << The Journal Name >>, but if there has been a change in style the units can be included.

The bigger issue is if the reviewer is confused (or believes the reader will be confused) and that providing units will clarify the confusion. If this is the case, then not providing units is a big deal. In this case I would provide units in terms of fundamental dimensions (e.g., length instead of meter and time instead of second).


In the US, many professors really don’t like the idea that students tremble in fear at any interaction with them, and/or regard them as a class of semi-divine beings who need to be constantly flattered and paid homage to. Any idea that the student’s actions are motivated by ideas like

“hierarchy”

“I should not bother to send another email unless it includes a considerable amount of new information”

“I should almost always send the last email”

“professors can ignore me but I cannot ignore them”

“lower people are expected to show more respects and do more works to maintain the relationships”

“Is it impolite to not to respond to professors' replying email asap?”

etc

will be seen as upsetting and in many cases offensive to such professors.
The standard etiquette in the US is therefore to treat the professor with the same respect and professionalism that you yourself expect to be treated with (and that any professional person ought to expect to be treated with) by anyone in a professional working environment. That is, if the context of the email requires an urgent response, then you should answer with a corresponding urgency and immediacy; and if it doesn’t, then you should answer within a time frame that makes sense for that context. The fact that you are a student emailing a professor has no effect on whether the time interval to answer an email is polite or impolite.


At which part of the paper is it better to cite R packages?

You should cite the software packages that you use just like any other piece of scientific work that you build on. If they are significant enough to make it to your main narrative, then cite them there just like the other key techniques you build upon. If they are useful but uninteresting methodological detail (e.g., equivalent to a microscope model or reagent brand) then they should  in just the same way be relegated to an equivalent methods section, appendix, or other piece of supplemental material.


What should be included in a departmental email policy?

Do issues like this really need a policy to govern them?  If someone in a department has a problem responding to emails in a timely manner, it seems to me that it would be better to counsel them directly.  Creating a policy for it may come across as passive-aggressive.

Corporations may have formal policies about how to answer email, and how to organize your desk, and how to change the toilet paper in the restroom.  But academics are used to a considerable degree of autonomy, and dislike being micromanaged.

My humble opinion.


Including teaching statement in RA position application package

I wouldn't hold it against anyone personally, but it could be bad or it could be good. If there are teaching or training opportunities as part of the job (like there are for people I hire), then it might be marginally helpful. It at least indicates an interest in the ancillary functions of the role. However, if it's a pure research position unattached to an organization with no possibility of a teaching role, a particularly unkind or paranoid sort might hold it against you since it could serve, to them, as an indication you'd prefer a professor/lecturer position, and that you are likely to not stick around very long if you can find one. This kind of stuff matters a lot more to some folks than it does to me personally. There's some legitimacy to this kind of thinking since the hiring process is time-consuming and expensive. You don't want to lose someone shortly after getting them on board.

My recommendation is to stick to the requested materials and no more. Tailor your application, CV, and letters to highlight the things that the position description wants.


Writing a letter of recommendation for your own, new grad student?

Several months, if you worked with the student, is plenty of time to get an informed impression, and especially so if your impression is good. This is how I would proceed:

Write how you know/met the student. Explain why/how your interaction developed. In your case, how did the student capture your attention, why you hired the student, what were the motives for this.

Then write facts. You say the student is terrific. What are the facts that support that? For instance, "the student solved a difficult problem in short time. The student very quickly understood the material you gave her to read. The student has produced a publication. The student is going to submit some research proposal earlier than expected. The student is extremely effective in running studies". Or, whatever is relevant in your case. At this stage, only list facts which are relevant to support the case of the student. If the student did not yet work with you, but you know the student from teaching her in class, you could go for "top 2 out of 50", "best coursework I have seen" or whatever is relevant there. Don't be tempted to write about things you do not know. If you have few, but promising, facts, limit yourself to state these and make them compelling.

In the next section, most references are expecting a few words outside of the concrete scientific facts, e.g. team work abilities, presentation skills, or something else of relevance that makes clear that the student has potential. Sometimes, hobbies are mentioned, but I typically make that dependent on whether it is relevant to the position/grant.

Now summarize your impression about the student, supported by the facts listed above. If you are delighted/looking forward to work with the student, do not hesitate to let that be known.

Of course, you would want the money - but, see it from the point of the funding agency: it is, of course, more likely to feel more confident giving the money to a student whose supervisor radiates the message that she is enthusiastic to work with that student. It is perfectly legitimate to support one's own student, and your reference will, of course, be completely open about that.


Good methods for creating high quality scatterplots

I'm not sure this question fits well here on academia.SE, but if you want free, beautiful, and powerful, it'll be hard to beat R. See e.g.

http://www.slideshare.net/dataspora/a-survey-of-r-graphics

http://www.sthda.com/english/wiki/ggplot2-scatter-plots-quick-start-guide-r-software-and-data-visualization


What to do with a likely collaborator who is not answering mails?

Presumably your prospective collaborator expects something more tangible than email discussions to come forward soon. So far, what you describe sounds fairly typical - material and ideas are exchanged, and papers are read (or not). However, at some point this needs to move into a more concrete direction than "discussions". That is, you are now in the phase where the pedal needs to hit the metal - somebody, presumably you, now needs to come forward with a concrete action plan or at least steps towards such an action plan.

Otherwise, if the discussions still remain on an abstract level even after multiple months and many emails being exchanged, I could understand that your collaborator fears that they may be wasting their time in this.

So the next step if you want to go forward with this would be to set up concrete next steps: arrange a planning call or even a visit, and then come up with concrete research methods and a methodology to address them. Particularly, be explicit about what you expect from the collaborator - the fact that they were not able to read your papers until now suggests they will be unable to contribute a lot of time, and it is better to clarify how they can contribute early rather than mid-way through the project.

I feel it is important to understand what the power and group dynamics are in such a collaboration. Why is everybody in the project? Who expects to get what out of it? Who is pushing / leading the project? Who has how much time to contribute, realistically?

These questions are all fairly different depending on whether you and your collaborator are students or senior academics. That is, if you as a student cold-mailed a senior professor the collaboration will ultimately have  different dynamics than if both of you are students, or both of you are similarly-senior academics.


How to improve my English from Academic papers?

The old adage is: "the language of science is bad English" (and at least in computer science it is 100% true). That being said, I have known PhD students who have failed mainly because of their lacking English language skills – they had ideas, but they could not communicate them to anybody, and they could not write them down in a paper for the life of them. You need decent English to write any paper, and you need pretty good English to write papers at top venues.

You ask how to improve your language skills from reading papers. I would say, you can't do that effectively at all. Clearly, reading anything written in English will help you to some extent, but if you feel like you need to improve your English, taking one or more (good) courses in technical English will help you more than reading through a few dozen papers.

However, there is one language-related skill that reading papers for is really useful – if you are setting out to write the first or one of your first papers of your own, nothing beats analyzing existing papers (at the same conference, in the same journal) to find out how papers in these venues are usually structured. This gets you started much faster than drafting something only for your advisor to tear it apart.


Is this a good enough reason for not taking an educational loan?

These are subtleties that could easily get your application dismissed on formal grounds. So the best thing you can do is talk to the appropriate department in the LSE directly. They may tell you it is ok, or they may point you to other options for taking educational loans. But they know (make) the rules, and we don't.


Differences in opinion when teaching a course jointly with another instructor

There are some things which are unclear in your question. However, I'm going to make a few guesses and if any are wrong then you might want to disregard this answer altogether.

It sounds like you have more education but less teaching experience than the other instructor. If you are new to teaching, one very common issue that new teachers often overestimate students' abilities. If the other instructor has more teaching experience then you might be better off 'going with the flow' for this first semester.

Another reason to go with the flow is, as Chris Gregg pointed out in his comment above, students once given a syllabus should not have it changed on them mid-stream. It's bad enough (for them) to have to deal with a change in instructor, they should not also have the syllabus changed on them as well. Consider what you could learn from the way the other instructor designed the course - we can learn things from those with less education than us.

I don't know what you mean by treated like some kind of stocks in a bursary market but, of course, without students there is no point of teaching so, yes, they are important. Nobody wants a large group of students to leave.

So, my suggestion is to try one semester following the other teacher's guidance and next semester consider taking everything you know, and everything you learned, and improve things.


Where to continue my research-oriented studies after Bachelor's Degree in Computer Science?

The reason why you're not seeing scholarships for study at the master's level in Europe is that the master's degree is not viewed as the prerequisite for PhD study, but instead as the direct continuation of the bachelor's degree. As a result, you're expected to move on to the master's program, and usually at the same location you did your bachelor's degree. That means there really isn't a call for a lot of scholarship to fund master's study. However, it is possible to finance one's stay in a European university, as many schools offer part-time positions for master's students working in a research group for some number of hours per week.

However, in the US and several other countries, gaining admission to a PhD program is a good way to get your master's studies funded, as the funding is normally provided for the entirety of your graduate tenure, rather than just the PhD portion.

To get in to most programs in English-speaking countries, you will need to show evidence of a good scholastic record as well as good English skills, as evidenced by the IELTS or TOEFL. If those aren't in place, it's going to be very difficult for you to be competitive, and almost impossible to be competitive for a scholarship or fellowship.


How to refer to a theorem in a book of which I don't know the source?

Contrary to intuition, it is often inappropriate to try to cite well-known and foundational material to its original source.  The reason is that you did not actually learn the material in its original form but instead from some modern reinterpretation of that material (e.g., in a standard textbook).

To see why, try reading the original for something like Newton's Laws of Motion.  First of all, it's in Latin.  Even if you get a translation, however, you'll find that the notation is strange and difficult to comprehend.  That is because even though the fundaments of Newtonian physics have not changed in the centuries since it was discovered, we have improved greatly in our ability to understand and teach the material, as well as in how we integrate it with other material.

In short: if it's textbook material, it is most honest to cite a textbook as your source.  Two modifying notes, however:

It doesn't have to be the textbook that you personally learned from---any good presentation will do.
You only need to cite a textbook if some of your audience may be unfamiliar with the material. In a computer science paper, the halting problem needs no citation; in an interdisciplinary paper expected to be read by e.g., economists or biologists, it does need a citation.


How should I email my graduate advisor if I did not hear anything?

It sounds like he is stressed and a bit disorganized.  Take pity on him and write again.  "How's it going, do you have some time to meet this week?"  Something like that.


What's the formal name of 'search committee' in a cover letter for postdoc application?

Can I just call it "Postdoctoral Search Committee"?

Yes, that's fine and normal in your situation.
If a specific person is named in the advertisement, use their name.


How do researchers ask others for comments and advices for their research?

A friend of mine wrote an undergraduate thesis that was groundbreaking original research.  Nobody at his university had the expertise to evaluate it, but one of the faculty suggested he send it to a fairly famous professor at another university.  He did.

That professor read his work and sent him some feedback, including several (correctable) errors he noticed.  He also made sure my friend's application to his program was approved and he was offered their best fellowship.  Eventually my friend attended that doctoral program and the professor he had contacted was his advisor.  He also published the a journal article based on his undergrad thesis in one of the leading journals of his field.

This is an unusual story; most "self-funded" research is not of that quality and many famous researchers don't bother to read that sort of email.  If your work is of that kind of quality, and if you are lucky enough to find a researcher who opens and reads it, this approach can work.  If you believe you're in that situation, definitely do send the manuscript in your initial email (or post it online and provide a link); the likelihood that the researcher will follow up and ask you for a copy, when he/she has no evidence of the quality or relevance of your work, is extremely low.

Always start with a salutation; the last thing you want is to come across as being rude.  I would keep the email short, but long enough to show the researcher that you've done serious research and that it's relevant to his/her interests.  Roughly the length of an abstract, though in your email you can describe things less formally and point out specific connections with the recipient's work.


What to do if you forgot some proofs while writing your thesis?

This is not a genuine problem. Everyone forgets things. A true scholar may nor may not be blessed with an exceptional memory, but the operational issue is about having personal resources that accommodate one's limitations, and sufficiently point to the relevant resources. So: self-management.

It is true that having a good memory, or an exceptionally-good memory, is generally an advantage in knowledge-based enterprises, obviously, but things are more complicated than memory-per-se.

And, in any case, being able to reproduce fluently all the basic things on a moment's notice is irrelevant. True, a certain fraction of more-senior people happen to have the sort of memory that allows them to reproduce certain things on-the-spot, but this is really not relevant to professional practice.

Yes, the most conflict-laden point is that faculty teaching graduate-level courses, and who've had the misfortune to have either a deterioration of memory, or have always had some memory problems, have difficulties with teaching. Not that they don't "know math", but that the details are not easily present in their minds. The other point is that this does not mean that their critical/critique-ing faculties have deteriorated. An awkward state...

But/and, after all that "too much information", the point is that no one (no professional mathematician) is required to be able to reproduce everything upon command at every possible moment.

(The whole "final exam" or "contest" concept of mathematics greatly and sadly corrupts our collective concept of that the thing is.)


First - a meta comment. Getting out of abusive relationships with one's advisors can be really difficult, especially if said advisor is a big name researcher. That said, once the first signs are in, it is often better to cut your losses and get out of this relationship than to stay on in a bad situation.

I think that if you have some real complaint then you should make your case to the department administration (head, dean for graduate studies etc). If your university has student support resources (e.g. a student union, an ombudsman), get them involved as well. What happens next is very dependent on the advisor's status within the department, and on your department's administration.

If yours is not the first case, then your complaint can have serious repercussions towards your advisor. Informing fellow students about this person's behavior is also a viable strategy, as it may protect them from a potentially terrible experience.

The weight given to your complaint is highly dependent on what it is that you're actually complaining about. If your advisors gave you bad advice but otherwise kept their advisory roles (e.g. regularly met with you, provided you with necessary resources etc.) then this could be chalked up to style/bad luck. A lot of administrative matters are beyond your advisors' control, so maybe what you perceive as a failure on their part really has nothing to do with them. If you have written proof of malicious intent or gross incompetence, then you may have a case.

Since you have already graduating, I see no benefit to you in complaining, at least under a very narrow definition of benefit. There is some satisfaction in knowing that you made the world a better place by acting against an abusive/incompetent advisor, again, under the premise that your complaint has real merit.


Why do many recent open access “mega-journals” only cover biological sciences?

I think one of the major issues here has been the existence of arXiv in all its various incarnations. Since there was already a major open-source distribution network—even if it eschewed important parts of the publishing process like peer review—it made the need for a PLOS|One-like journal much smaller.

A secondary issue is that many of the journals in the mathematics and physics communities have fairly liberal policies on the use of open-source repositories to distribute papers; for instance, the American Institute of Physics and American Physical Society allow publication within their journals, while still allowing authors the right to "self-publish" using their own version of the materials. Similarly, the American Chemical Society, while having slightly more restrictive policies than AIP or APS, still effectively allow open access after one year of "exclusive" access.

So, ultimately, I think the emergence of PLOS|One and similar efforts is an attempt to move more in the direction that already exists in the various physical sciences communities.

Edited to add: One additional issue that may explain the state of activities are some of the recent decisions by the NIH to require that manuscripts published with NIH financing (thereby including the majority of biomedical research in the US) had to be made publicly accessible within six months of publication. This is a development that has not been matched by the NSF and other major funding agencies, nor is it a rule in most of the European Union, as far as I can tell (although I believe the UK is haltingly starting to move in that direction).

As a result, there is a strong impetus for open-access in biology and biomedical science that is not matched by the other fields (which might not have nearly as much money and therefore would not have the clout of the NIH).


What should I do if I have an idea but can't work on it immediately?

Now you are a postdoc and not a graduate student anymore. As such, you will have many research ideas, that you will not have the time to implement yourself. So, it is time for you to start delegating this work to "less experienced" workforce than you. That means undergraduate, master or PHD students. So, you should discuss it with your advisor that you have a new idea and that you are planning to propose a new undergraduate or MSc thesis. Perhaps he might even propose, working with a graduate student who is a bit stuck at his current stage of his / her PHD, so working in your new idea might be beneficial to both of you.

In any of these cases, co-authorship issues should be discussed early and thorough. For undergraduate, MSc students usually the assumption is that they do most of the work (it is their thesis after all) but you write the paper and you get to be first author. For teaming with PHD students, things are a little bit trickier, so these issues should be discussed in detail, BEFORE the cooperation begins. Also, make sure that your PI is OK not to be included in the subsequent publication (since this is your idea after all). Of course, if you want to include your PI in your "additional" publication then by all means, go ahead (this will also help you bend his objections about the time you will spend on your new project). But if you do not, make sure you discuss it before doing it, so you will not get into hot water.

In this scheme, not only you can multiply the number of your publications more easily and faster but also you help other people, who might be your future collaborators. So, you really have nothing to lose.


How to find help when writing a master's thesis

At the end of the day, your advisor is the one who needs to accept your thesis. Seeking help from others may be useful for some types of questions, but you'll definitely want his feedback during the process to make sure you're developing the thesis to his standards.


What does this professor mean by saying "I do not have time to respond"

Keep in mind a very simple rule: Professors are human beings

Many of the questions on this site seem to assume from the outset that faculty are strange, mysterious and mercurial creatures, whose motives are entirely opaque and whose every word must be subjected to an intense amount of kremlinology.

"Sorry, I do not have time to respond." means that he doesn't have time to respond.

There could be many reasons for this. He might be particularly busy at the moment - lots of conferences take place in the summer, and many academics also use it to catch up on work not done during the academic year. If he is, as you say, approaching emeritus status he may be occupied with wrapping up things he's intending to walk away from. He might be dealing with other things in his life.

You should take that message at face value, and try not to impute any sort of hidden motive onto it - you simply don't know enough to know. Try following up in a month or two with a simple question as to whether or not his schedule has freed up and he might have some time. If the answer is still no, let it go.


How competitive is it to become a tenured history professor at a four year institution?

My wife is a historian, and I can attest: it is extremely competitive.  The basic reason is that many more people are earning Ph.D.'s than are being hired to tenure track positions.


When do you expect to hear back from NSF (DMS)?

The time to hear back on an NSF application is highly variable, both by grant vehicle and for individual applications.  Since most NSF grants are peer reviewed by a panel of academics who also have to meet in person, there's a significant length of time naturally built into the system.

Another part of the delay is that for most programs there are very few applications funded.  As such, even though there may be many clear rejections with relatively fast responses, program managers may end up having a long fight to find sufficient money to accept a project that is right on the boundary of getting accepted.

Still, if you're looking for a number, I have personally never heard of a NSF grant response taking less than 3 months or more than 12 months.


Can a graduate program rescind my offer if I don't complete a previously declared Minor?

I...declared a 'Minor in Computer Science (Expected)' on my US graduate school (PhD) applications. I have been accepted by a couple of programs...[C]ould [acceptance] be rescinded for not [achieving that qualification].

It depends on the offer. If an offer is conditional on the basis of you achieving a minor, then, yes, that offer can be rescinded. Otherwise (the offer is unconditional), it cannot. (Conditionality of an offer may be buried in the fine print.) Albeit, we're in legal territory and INAL.

For practical purposes, I suggest that you contact the universities that have made offers and discuss your situation with them.


How much should I worry about British spelling when submitting to a U.K. journal?

The answer depends very much on the journal. Some expect UK spellings; others will permit either American or British spellings. You should check with the journal in question.

Of course, the other option that you have is the following. Since you know what the major differences between the two sets of spellings are, and you have a sense of which one's won't be caught by your spell checker, you could always do a final search-and-replace after you've completed work on the paper to make sure you've switched everything over. (Or at least, everything you know should be switched over.)

That should satisfy most journals, and as shan23 said, I don't think a journal will reject your paper for writing "meters" instead of "metres"; the most you'll get is a referee report telling you to switch spellings.


In general, it can mean one of two things:

Your title. For example, Dr., Rev., Arch., Atty., Engr., etc.
Your job title. For example, Head of Gastrointestinal Surgery, Parish Priest, Associate Professor of Global Health, etc.

It really depends on the place in the application in which the information is being sought and for what use.

Anyway, good luck!


It depends on the school. My undergrad institution, for example, went out of the way to try to pull transfer students into the fold. While I was not a transfer student, I worked closely with the orientation department and this was a big push on their part. However, it usually comes down to the individual student. I suspect that many transfer students are perhaps overly self-restrained upon transferring to a new school and thus don't reach out enough. So, as @RoboKaren pointed out in the comment above, transfer students are often left behind.

A great piece of advice I was given about college (and grad school) in general was "you're paying for it so get your money's worth." I admit this doesn't perfectly translate outside the US where you may not be paying for it directly, but the sentiment is the same. You're spending your time (and possibly money), so be proactive. Ask questions, make a concerted effort to get to know the professors, etc. Faculty probably couldn't care less that you transferred as long as you're interested and/or talented in their pet field. If you make a clear effort to do this, whether or not you're a transfer student will make zero difference.


What is the difference between a research paper and a student paper?

A research paper is original work and could be written by anyone with the background.  A student paper is a research paper written exclusively by student(s).  The reality is that faculty will be involved in some way, even if it is only running the research program which made the work possible.  In reality, the faculty will be more involved than that: discussing, reading and suggesting.  But that's part of the job, in my opinion.


This seems like a great opportunity, actually. If you can go visit him in the office just ask if the gift card offer is still open. He will probably slap his forehead for forgetting about it. Keep it low key. But it is a good thing to make a connection like this. Even bumping in to him in the hall would be a way to raise it.

If you can't visit in person, an email would be fine. Just remind him of the question you answered and ask if he forgot about the gift card or whether some issue came up. Just be direct. You don't need to be bashful about such things.

Edited to add: It would also be good, no matter how you do it, to thank the professor for the problem you solved and for the offer of the gift card. The reason for thanking him for the problem is that it, I hope, increased your learning.


Where should I put the "Definition of concepts" section in a Research Paper

Conventions like this vary between fields.  Look at other papers in your field or subfield, and do what they do.


Leaving PhD for a professional master's program

I have sat on admission committees, taught in professional and graduate programs, and written recommendations for undergraduates, masters, and PhD students to go to professional programs.  That said, my experience is with programs in a business school. Depending on your program of interest, what I say may not be relevant.
For masters programs in a business school, your profile is not unusual. Lots of MBA and business masters programs see people who finished a PhD and then decided they hated it, sometimes after years and sometimes right away. We also see lots of applicants who are giving up on a PhD to pursue an area they now find more interesting.
In my experience, students who did a PhD or left a PhD program tend to fall into one of two camps: excellent students and so-so to poor students. The best bet to separating these groups is motivation.
The students I typically saw do very well were people whose interests shifted, had clearly worked hard before, and were excited about their new area. The people who did not do well were people who had sort of "failed out" of the PhD, had not made progress toward a PhD for years, or were not succeeding at post-PhD work. Often, these students were not excited about the program they applied to; rather, they applied just because they needed a job and this sounded like the way to get one with the least work.
I think your key is making sure your recommendations convey your enthusiasm for the new program -- and to also express that convincingly in your own letter. It may also help if you can use your academic contacts to chat with professors in that program. Your advisor may be helpful... or may abandon you since you are no longer targeting academia. You are probably the best judge of which of those is most likely.
Finally... congratulations for giving thought to whether the PhD is right and healthy for you. I know plenty of people who just pushed through and then ended up repairing the damage that caused with years of therapy.


Tutoring is depressing because my students are struggling too much with my exercises. What do I do?

What you're experiencing is pretty much what all college teachers are wrestling with all the time everywhere.

Allow me to point out that the abyss of need can go much, much deeper than what you're currently dealing with. In the U.S., most college students are attending a community college. And most students entering U.S. community colleges do not have 8th grade algebra skills, nor even 6th grade arithmetic skills (e.g., fractions, proportions, negatives, estimations, times tables). I've had a good chunk of a college math lecturer career at this point and I've never taught anything as high level as matrices.

Here's how I've been able to jiu-jitsu it in my own mind. Think of it like a diagnostician. Doctors have to find it fascinating to track down hideous diseases. Detectives have to find it compelling to decipher ostensibly horrible crime cases. So too: I find it endlessly fascinating to diagnose what exactly is the block or problem in students' heads, or to track down the place where their reasoning first went off the rails. Ask questions to try and find where their reasoning starts and where it stops. Do something of a binary search to try to narrow down the problem spot. I'm continually discovering new gaps in people's knowledge that I never would have expected. It's surprising and amazing every day.

Usually I do find that students simply cannot remember starting definitions. If they've come up through a system that depends on raw faith and memory (and not mathematical reasoning), they don't get how important that axiomatic basis is. Many also clearly have learning disabilities that make this difficult for them. "All your answers are back in the definitions", I say several dozen times per semester. Have the book handy so you can turn back to the starting definitions at any time, and see if they recall or can see how their reasoning got off track that way. In fact -- this explains why at your current school they're asking students to reiterate definitions; whereas for us that's natural and obvious, for some it's an overwhelmingly difficult blind spot to fill in.


Discussion of hiring practices and underrepresented groups during interviews

Discussions about how to improve participation from underrepresented groups in academia are not uncommon in interviews, even when the interviewee does not come from such a group.  That a department has a strong commitment to hiring people from underrepresented groups is an important thing for the interviewee to know about the department.  After all, if the interviewee is hired, they are going to be expected to be part of the departmental team that is working toward broadening participation.

If you are interviewing for faculty positions and are not part of an underrepresented group, it is still a very good idea to have thought carefully about the underlying issue.  When the issue comes up in an interview, you should be able to voice your support for broadening involvement in your field.  You should also have some specific thoughts about why this in important and, most crucially, how you can help.  Hiring you may not represent direct progress toward the goal, but you have an opportunity to show that you are enthusiastic about recruiting students from underrepresented groups and working to hire people from those groups when you are part of the faculty.


Withdrawing conference submission before notification

Yes, you can withdraw it. There is no issue. The paper is yours. With a month to go you will cause little disruption.
Sooner is better, though.


Generally speaking, a poor way to handle such situations is to divide up the work to individuals and then try to assemble the whole at the end.

If the group is reasonably small (say five or less) try to have regular meetings to brainstorm and outline things for the report. One person (probably the one with the best language skills) takes on the task of editor, or even writer.

Pass drafts around frequently and update them based on feedback.

If the group is larger, then do some division of responsibility, but to sub-groups, not individuals. Have each subgroup work as suggested above (brainstorming...editing...markups). But then, one or two people take on the task of getting everything together. Those two people need to monitor and shepherd the task throughout, making sure that the subgroups are doing their work productively.

It might even be advisable in a long project, to shuffle the groups a bit periodically. Not a radical reshuffle, but just some cross pollination.

You should also expect, and plan for, the fact that not every member will be able to contribute as much as others, or even at all, for various reasons, both legitimate and not. But just as important, don't set it up so that everyone needs to contribute in the same way. Try to draw on individual skills. Some doing research, some writing, some editing, etc.

A team should be a team, not a herd of individuals.

This might be different in a different field, but for an MBA it feels about right.


Reporting yet-to-be completed graduate study on CV

I would recommend a slightly different phrasing, to explicitly stating the start and expected duration of your program:

  XYZ University, PhD, (2014 - 2019 [anticipated])

This conveys clearly the important information of how far along you are in your doctoral studies.
Most people know that there can be a great deal of variation in the completion of a Ph.D., and nobody expects that you can predict the future, so if you later shift the date forward or back, it should not be taken amiss by anyone reading the C.V.


Will a graduate student publishing in different disciplines confuse potential employers?

The only real danger you will have with prospective employers (presuming that you look for a postdoc before your faculty search) is that a potential advisor might be concerned that if you aren't engrossed in their research, you will seek out opportunities in other areas. If it's their money that's supporting your time, then you'd be expected to devote your effort to the line of research you've been hired to do, not what you'd like to do.

This is something that you'd have to explain in your cover letter in any case. But you'll need to explain—as you have—that your lateral move was encouraged and done with the support of your current advisor. Otherwise, it could be a concern.


Resolving authorship when PhD student does most of the work on paper, but originally agreed to support another PhD student (first author)?

I personally find the "* authors contributed equally" footnotes to be supremely awkward, though perhaps you're in a discipline where they are common, in which case go for it....  And in this case you're arguing it isn't even true.  I'd say you're getting a raw deal, but the time to push back was earlier, when you could have argued for the appropriate recognition and then declined the chapter inclusion if you didn't get either the proper recognition or more work from your colleague.

My advice: treat this as a learning experience, be gracious, and move on.


PhD salary and teaching assistantships in German-speaking countries

I can only speak for Germany:
Teaching is done by professors. Sometimes they delegate certain courses to assistants (not TAs, usually PhD candidates or post-docs), but this is still counted as "teaching" by the professor (there are legal issues involved which I don't want to adress here, but this is the common practice). As a consequence, the assistant gains teaching experience (which is good and might help in further career steps!), but there is no additional financial compensation.
Usually, PhD candidates are hired for certain research projects or they are assigned to graduate schools, in both cases there is a salary / scholarship financing your work. In my discipline (computer science), this is less then a job in industry, but it's not bad (you might want to look up TVL-13 here). It depends on the culture of your discipline if you are getting a full salary or just 50% (in biology I heard there are people getting even only 25%).
In addition, universities might hire external visiting lecturers who are recieving up to 55€/hour, but at my university we were forced to lower the rate to 35€/hour (teaching hour = 45 min.). But usually those people have to be external, you can not be employed by the university and get this salary on top.
But in short: If you are getting a position in a funded project, funding your costs of living is not an issue.
BTW: Teaching can be done in German or English, depending on your University and course level.


Can I use someone’s answer from a StackExchange site in my publication (journal paper)?

You should consult the Stack Exchange Network Terms of Service and read through the section 3. Subscriber Content which concerns rights of the material posted on the site.
I will specifucally reiterate the following

In the event that You post or otherwise use Subscriber Content outside of the Network or Services, with the exception of content entirely created by You, You agree that You will follow the attribution rules of the Creative Commons Attribution Share Alike license as follows:

You will ensure that any such use of Subscriber Content visually displays or otherwise indicates the source of the Subscriber Content as coming from the Stack Exchange Network. This requirement is satisfied with a discreet text blurb, or some other unobtrusive but clear visual indication.

You will ensure that any such Internet use of Subscriber Content includes a hyperlink directly to the original question on the source site on the Network (e.g., https://stackoverflow.com/questions/12345)

You will ensure that any such use of Subscriber Content visually display or otherwise clearly indicate the author names for every question and answer so used.

You will ensure that any such Internet use of Subscriber Content Hyperlink each author name directly back to his or her user profile page on the source site on the Network (e.g., https://stackoverflow.com/users/12345/username), directly to the Stack Exchange domain, in standard HTML (i.e. not through a Tinyurl or other such indirect hyperlink, form of obfuscation or redirection), without any “nofollow” command or any other such means of avoiding detection by search engines, and visible even with JavaScript disabled.

Apart from the specific points in the Stack Exchange Terms of Service, normal courtesy and etiquette involves always providing credit where credit is due. Even if someone posted information saying it is free for all to use, it would be appropriate to at least acknowledge the contribution by that person. In the (I assume) hypothecial case you describe in your post, contacting the person would seem like the best approach. First off, it is better to be safe than sorry, Second, by contacting the person you can avoid misconceptions or misunderstandings to accompany the post into your work and the integration fo the original idea into your work can improve. If the person upon your contact says, run with it, then fine but then you know.
So apart from avoiding to break the stated rules it is always good to contact the source and be open about the intended work or use if you work on material to be publically available through publication or otherwise.


Do I need a conference paper to vouch for a tool I built in my undergrad when applying for a PhD?

Having published a paper does have a positive impact on PhD applications. (But you don't "need" one in the strict sense - it is quite possible to get into grad school without having published.) But the reason is not because it "vouches for" your tool working. In most cases, the reviewers never get to try to execute your code, so it can hardly speak to that.

It does, however, indicate your ability to produce something novel, of interest, and to describe it in a manner that receives the approval of other scientists in the area - in other words, your ability to do research. Which is exactly what the PhD admissions committee will be looking for.

Whether you think that is worth the conference costs is a matter of personal judgement - but you should first look for other avenues of funding, such as your advisor or a travel grant from your university or the conference or a third party promoting undergraduate research etc.


What is expected in a masters thesis of a mathematics student?

I think this varies a lot. But for Germany your first question can be answers succinctly: In a Master's thesis you should show that you have potential for research.

On the other hand, expectations vary a lot between advisors. But certainly you do not have to prove a new theorem or develop a new theory.

  How much is it valued (if at all) when one applies for PhD?

I can only answer for the situation where you apply in Germany. The thesis can be a door opener if it is topic closely related to the field where you want to do a PhD. Also a good mark is important. But also in Germany hiring professors will often contact your advisors or request a reference letter and this is much more important.

  I have heard that its value is more in Europe than America, which if I were to guess I would say, may be due to no GRE like criterion. Is this true?

Not sure on this point since I can't provide a comparison with the US and also I am not sure if the situation is uniform with the EU.


Paper accepted at a probably predatory conference, how shall I proceed?

Don't go.

You write that it's a valuable experience to attend a non-undergraduate conference, and it would indeed be the case, but you won't be attending anything like a non-undergraduate conference. Example story, and that actually reads like one of the "better" predatory conferences, since I've read about other predatory conferences where keynote speakers don't show up and attendees talk about completely unrelated stuff (e.g. a number theory talk at a food science conference).

This kind of event won't help your CV either, because if someone checks the conference out they'll discover that there's no quality control, meaning the quality of whatever you presented is now suspect.

Since you gain nothing by going, is there still worth going? Possibly, but any reason for going would be much less tied to the conference than to other things, e.g. perhaps you know someone who lives near the conference venue and have been looking for a reason to visit. If you don't have these reasons, you might as well save on the cost of travel.


How do academics with teaching responsibilities, etc. find the time to do research?

How does anyone "find the time" to do anything? The answer is that mathematicians don't "find the time", the time is already there and they make use of it. Your premise that those other activities you mentioned already fill up 100% of the time is simply incorrect. In particular, summers, breaks and other periods with no teaching offer a convenient and relatively distraction-free environment for doing research. But even teaching is not mutually exclusive with doing some research.


How does one become an Affiliate Professor?

A wide range of "Affiliate" and "Visiting" titles are often used to simplify bureaucracy in a long-duration academic interaction.  For example, you may have a collaborator who frequently visits, and want to give them access to buildings, networks, and other resources so that their visits are less of a hassle for everybody.  A "Research Affiliate" or "Affiliate Professor" or such status allows the institution to officially put the person into the system so that they can be issued keys, ID cards, access permissions, etc.

The mechanism for actually doing this is typically that a sponsoring professor just calls the appropriate department or fills out a form, and it just happens.