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Should I apply again to the same research group where I used to work and haven't got any PhD offer from the professor?
Approximately a couple of years ago I was working in a Computer Science project abroad. The task was to implement a software analysis tool with the collaboration of a professor, and if all went well then I could get a PhD position at one of their departments.
Well after expending like half of the year on the project, due to some personal problems that did not allow me to focus entirely on the programming task, ie. taking care of my old parents, it was that the project suffered a delay.
When I was about to end the project and got some finishing results, the research was published in another country by other university. It seems here that the phrase "publish or perish" was more real than ever. Because of that reason the professor in charge did not offer me the PhD position, so I was some sort sad about it.
I have the inner feeling that I could have done better to get that position, so I don't know if I should ask to the professor in charge if he could give me another chance. Maybe if I do that I will bury myself academically, but I don't know what to do.
Any advice?

Does the professor know the reason for the delay?

You got scooped. That sucks, but it happens a lot; and it is definitely not the end of the world.
If you think your work was good in the group, I would say go ahead and apply. You could explain to him why the project was delayed; a polite discussion cannot possibly hurt you, and you can figure out in which terms they are with you. Remember that even if you were in your best conditions, some other group may have just more people working on the same problem, or they started one year before you, or any other reason.
By the way, you have now a working implementation of the analysis, and perhaps you can improve it to do something the other group didn't; implement other algorithms, etc.

You could explain to him why the project was delayed - Just don't make it sound like a poor excuse.

@flo absolutely! And maybe "personal reasons" may even be enough detail.

@Davidmh In my experience, professors don't hear the excuses at all. They act like they have never been students.

@EnthusiasticStudent those are the professors you don't want to work with. It was good that you knew before enrolling! Most of the people I have worked with (and all of the ones I have continued working with) are not that way.

@Davidmh Do you think I should stop working with those professors?

@EnthusiasticStudent I know I don't want to work with them, and I have enough good options. But this is derailing, you should ask a new question.


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How to address graduate school recommendation letter?
Since I'm applying for grad school, I'm currently in the process of acquiring recommendation letters from my professors. They usually ask me a few questions about how to guide the letter, such as what do I want to emphasize and how to address the letter?
How does one address a grad school applicant's recommendation letter? I mostly settle for "Dear Madam or Sir". Is "Dear Graduate Admissions Committee" or some other alternative considered better?

The header is the least of your concerns regarding your application. What they probably are asking you is what are your strong points, and how are you presenting them in your cover letter or equivalent.

@Davidmh thanks for the reminder. I do understand it's the least of my concerns, however I am curious if there is a standard or not.

I often use "Dear Colleagues" when addressing a committee whose membership I know nothing about.

According to Wikipedia

Dear Sir or Madam or 'Sir/Madam' (If the gender of the reader is unknown).
To Whom It May Concern (If the writer wishes to exclude the gender of the reader from the salutation and/or to convey that the reader should forward the copy to one more suited to receive or respond appropriately).

As @Davidmh has mentioned it is least concerned. I personally have chosen to use "To Whom It May Concern" when I applied to grad school as in some grad schools the recommendation letters might get forwarded from the admissions staff to various professors.
Edit : The first is British English and the second is American English as mentioned by @Davidmh

The first is British English, the second corresponds to American English.

If you are required to send your letter of recommendation to a specific person (may be your future advisor), the admission committee, head of department or an office in the university where you are applying to, then you should tell your professor to address that specific person or office. If in the guidelines of your application, you have not seen any emphasis on to whom/where should the letter be written, then ask your professor to write you a general recommendation like the one indicated in the @Srikanth's answer.
P.S: As I read the first paragraph of your question; I think your professors want to know what is most important for you to be included in your letter of recommendation. Something which will positively affect your application chance and something that should become bold in their recommendation. Of course they have many students in their classes and they may miss some positive and important points about you. So, they ask you to remind them the important things which comes to your mind. I have seen some professors that ask the students who want letters of recommendation to write a draft themselves and by reading the draft, they write a recommendation letter for their student.

Moderately off-topic, but is it actually appropriate to bold something in a recommendation letter?

@Seanny123 Not to really make some parts of the text bold. To make some indication in your recommendation, to highlight your positive points, to mention important parts.

I usually put the first occurrence of the recommendee's name in bold.

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Is there any difference between PhD and D.Tech?
Just out of curiosity, I will like to know if there is any difference (if any) in academic environment, between Ph.D issued by most Universities and D.Tech issued by University of Technology.

I think this is the first time I've encountered the "D.Tech." degree.  So its value might depend on the willingness of ignorant folks like me to go and find out about it --- whereas we already know what a Ph.D. means (or ought to mean).

According to Wikipedia, the nature of a D.Tech depends on where it is issued, and who by.  In some cases, it is equivalent to a Ph.D., in other cases it is definitely lesser.  It is certainly not a commonly issued or recognized degree, but that does not mean it has less value if it is from a strong institution.

Typically its awarded in only a few British Commonwealth locations. It was awarded in Australia once as a Professional Doctorate (Deakin Uni) - and as such was at 'roughly' the level of a PhD although Professional doctorates are often considered less 'academic'. In South Africa it is/was common amongst the University of Technology sector. They are considered similar to a professional doctorate - in that they are more practice based than a traditional PhD. In the UK itself however it was once common many years ago in the University of London as a Professional doctorate - ie typically done by working people. Nowadays in the UK it is common as either a Higher Doctorate - typically given to PhD's after they have established themselves via a body of public work such as books and publications and therefore is considered higher than a PhD. Otherwise it is commonly given as an honary doctorate to luminaries in fields related to Engineering or Science. BTW I have a BTech(Hons) and an MTech followed by a PhD from the UK. Perhaps when I am older I will submit my body of work for a DTech. All were from schools of electronic engineering, although its probably impossible to do that today. It was once common at universities like Brunel and Cranfield.

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Computational Physics or Engineering Physics, which deal with new technologies related to energy?
I currently on track to graduate with a B.S. in Computer Science and Physics. I am on the fence on which masters program I should pursue. I want to deal with new technologies like sustainable energy and things like Tesla motors.
Which degree would be more beneficial for the field I described or is there another engineering program that would better fit?

If you want a hands-on approach then Engineering Physics seems like the logical option, if, however, you want to think about the problems on a more abstract level, Computational Physics seems like the right choice.
Since you are doing Computer Science, you probably love, as many of us do, the power of coding languages, and might feel more comfortable using these to solve problems, once again that would mean computational physics might be more your thing.
The real question is how you want to deal with these new technologies. If you want to really work with these new technologies, I'd opt for engineering physics. You might want to take a look at some of the courses in these master programs and see which suit you more, or you could engage with master students of these courses to get a better insight in the course.

Thank you for your answer. I been looking int EE and EP, I am leaning a little towards EE but I am liking the curriculum of EP. Either way I can take Computer Sciece electives and still have a nice foundation.


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Good books/resource on mathematical writing
I am a freshly graduated Ph.D. I want to improve further my mathematical writing (in English, if this matters).
I am looking for books/resource that address good mathematical writing. I can find some books, for example, A Primer of Mathematical Writing by the AMS. But I wonder if there are any other new books or resources.

You do not have to. Wait how your first question turns out, and learn from it to improve the further questions. (I retracted my close vote, by the way.) Also, I think we can clear up the comments now.

As this is a resource request whose answers will be a list, I've made it community wiki. (That doesn't necessarily mean it's on-topic - the community may still decide to close this question, as often happens with "big list" questions)

I recommend the paper (series of class notes) Mathematical Writing, 1989, written by Donald Knuth ("Art of Programming" author, among other things), Tracy Larrabee and Paul M. Roberts.
Here is a description from Stanford:

This booklet records the class on Mathematical Writing led by Don Knuth at Stanford in 1987. Among the 31 lectures are guest appearances by Herb Wilf, Jeff Ullman, Leslie Lamport, Nils Nilsson, Mary-Claire van Leunen, Rosalie Stemer, and Paul Halmos.

We saw many examples of "before" and "after" from manuscripts in progress. We learned how to avoid excessive subscripts and superscripts. We discussed the documentation of algorithms, computer programs, and user manuals. We considered the process of refereeing and editing. We studied how to make effective diagrams and tables, and how to find appropriate quotations to spice up a text. Some of the material duplicated topics that would be discussed in writing classes offered by the English department, but the vast majority of the lectures were devoted to issues that are specific to mathematics and/or computer science.

It is helpful not just for mathematicians but scientists and technical communicators of all sorts.

Knuth, mentioned in another answer, is trustworthy and a good author.  The book mentioned by the OP maybe be useful to beginners, but I don't agree with many of Krantz's (the author) opinions about writing.  In general, people have various opinions and tastes about writing, so it's good to see a spectrum of opinions and determine what approach fits for you in a particular situation.  And now that you've started thinking about these things, read mathematics critically so you can build up examples of what you think works well and what doesn't.
Anyway, some other references are:
Terry Tao's advice on writing, which includes many links to pieces written by other authors
Milne's tips for authors, which includes a reference to Krantz's book and an essay of Hersh)
It might also not be a bad idea to read general advice about writing (not just mathematical/technical writing).

Also, while not specifically about writing, Rota's 10 lessons touch on a couple aspects of writing.

Coursera has a specialization called Reasoning, Data Analysis, and Writing Specialization I recommend watching the first three weeks of Think Again: How to Reason and Argue. You can consider the course English Composition I as well. There are other MOOCs dealing with your topics as well. Search coursetalk.com to find some MOOCs.

After reading the description, I must say I am sceptical that this course has much value for someone who already has a PhD and is specifically looking to improve their mathematical writing skills.

These two books are spot-on and I'm surprised they haven't been mentioned yet.
Handbook of Writing for the Mathematical Sciences, Nicholas J. Higham, SIAM,
https://www.siam.org/books/ot63/.
Writing Mathematical Papers in English, Jerzy Trzeciak, EMS Publishing, http://www.ems-ph.org/books/book.php?proj_nr=34.

Can you elaborate what type of writing?
For example, Joseph Mazur brings forward Euclid in the Rainforest, which includes mathematical concepts but is also in part biographical and simply an enjoyable read.
I am not sure if you mean tools such as Mathematica or LaTeX for symbiology ?
Or perhaps something like SHARELaTeX at https://www.sharelatex.com/learn/Mathematical_fonts ?

I have come across good book for Mathematical writing with the titleWrite Maths right by Prof. Radhakrishna.


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Publishing dissertation chapters instead of a monograph
I am at the end of my second year of a tenure-track position (my institution uses calendar years instead of academic ones) with a heavy load of service. This academic year I was assigned to work on six committees.
I defended my dissertation in 2013. I intended to turn the dissertation into a book but after three years applying to jobs while having temporary positions I barely could find the time to work on it. My mentor suggested to publish the dissertation chapters as journal articles since the book is not required for tenure and it has been the norm in the department.
I have mixed feelings about this but I know that with the teaching and service load it would be extremely hard to work on the book; especially since I will have to translate it – my specialization is Spanish literature and my thesis is in Spanish.
Should I publish the dissertation as articles and then think of a new project for a future book publication?

Would you publish the dissertation as articles and then think of a new project for a future book publication?

Yes, I would. Your mentor is right.

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Is it reasonable for authors and editor to ignore review comments without explanation?
I recently reviewed an experimental molecular biology paper for a mid-tier journal. I found the work valuable but missing some important controls, and recommended a list of major and minor revisions. A few weeks after submitting my review, I received an e-mail from the journal notifying me that the manuscript has been accepted for publication without any details or explanation.
Given the very short time between submitting my revision and the acceptance, the manuscript was either accepted without any change or accepted with very minor changes. So essentially most or all of my review was ignored, and I did not get any information from the editor or authors.
I find this to be very annoying and will probably not review for this journal again. My feeling is that if I invest my time in reviewing for a journal, the editor can of course decide as they wish but if they decide to ignore my review they should offer some explanation. Otherwise I am just a "rubber stamp" used to say the manuscript was peer reviewed.
My question is whether this kind of behavior by the editor is reasonable in your view, and whether you would ask the editor for clarifications (I probably won't, as it seems a waste of time)?

This might be field-dependent. Maybe add the field as a tag? 2. Do you know if the paper was accepted as is, or accepted but the authors were encouraged to revise it according to referee suggestions?

It never happened to me but there is space for such an occurrence. Perhaps there were two extremely positive reports. Sometimes we can miss the point of a paper by focusing on what we are doing (not that it must be the case). I would surely consider no to be referee for that journal, this is also true.

@TommiBrander thanks, I added mention of the field (experimental molecular biology) in the body of the question. I do not know whether it was accepted as is, but if any change was made it was very minor given the timeline (in my experience with such papers). But I will have to wait and see the published version.

Remember, your view of the process is incomplete. Don't jump to conclusions. For example, this could've happened: the editor sent the manuscript for revision, which the authors took a few weeks to perform. The editor was able to check the revision without needing your help, so they made a decision without inviting you to review the revision. You mention that given the "very short time" between you submitting the review and the decision, the paper must've been accepted without revisions, but "a few weeks" is not a short time.
Another, more drastic possibility is, during the review period the lead author died, and the none of the remaining authors were sufficiently motivated to perform the necessary controls. The paper then became a "either you publish this or it'll go unpublished" paper and the editor made the judgment call to publish it (you did say the work is valuable!).
I suggest saving your anger until after the paper is published. You can read it then and compare against the version you have. If you indeed find that the editor ignored your review, you can write to the editor then asking why they ignored your review.

Thanks. In my experience (given the field, the nature of my suggestions and my past experience with the process), this is a short time. But I agree that I will have to wait and see. What annoys me is that something like this happened to me in the past in a different journal, and there the paper was published without making a single change. I hope this will not be the case again.

While it is possible for reviewers to simply be ignored, I doubt that would be the case for a reputable journal. But, as you suggest, there may be a problem. But let me suggest that there are other explanations.
First, you don't know, really, that the "editor" is the actor here. And you don't know that your comments were ignored "without explanation". You might want to ask the editor about that, of course. But it may be that things just happened very fast - a few weeks. You don't mention that you have seen the paper, for example.
On the other hand my advice to authors is that (a) they should consider every reviewer comment for revision and (b) they maintain ownership of the work and all judgement about how to modify it. For those that take the advice, the implication is clear: you don't need to modify the paper based on any specific comment. But it is risky for that author to ignore too much that reviewers suggest and editors may not be amused by such behavior.
This can be a delicate dance, of course. A reviewer doesn't become a co-author. A reviewer just points out flaws and improvements from their own standpoint. An editor can, validly, choose to not include some reviewer comments to the author, though I suspect this is pretty rare.
But in addition to the author maintaining ownership of the paper, the editor maintains ownership (of a sort) over the journal contents. The editor can choose to accept (or reject) a paper at any stage to meet their own criteria.
So, a reviewer has ownership only over their own comments, not the paper, and not the journal.
Of course, you can choose not to work for them again, as there is little reward for it, but I'd suggest, at least, that you read the final version before deciding that you have a complaint.

Thanks. It is ok of course for the editor and authors to decide that any or all of my comments are not valid for some reason, but in that case I think it is reasonable to expect to receive some kind of feedback or explanation.

I think it can be reasonable. It is possible that the authors just rejected your criticisms (for example, because they did not have time to act on them), whereas the editor decided to accept the article because, according to you, it was valuable. I am not sure editors owe reviewers explanations of their decisions, as the rationale behind their decisions may be confidential. For example, their reasoning may be along the following lines: "Yes, the article is lousy, but not as lousy as my mid-tier journal":-)

Well, reviewers review for free, so I would say they are definitely owed explanations at least.

@wimi :  One might as well say that "reviewers review for free, so they are definitely owed money", and this statement can even be fair, but this is not how it works today. Maybe reviewers will indeed be paid in the future, but today we have to deal with the current practice. And again, I don't understand why an editor has to explain why they accepted an article that the reviewer deems valuable or to disclose confidential rationale behind the decision. One can say that the editor should lie in such case, just to be polite, but would that be more ethical?

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Rankings for university departments
The Internet is littered with information about university rankings and comparisons that it is very easy for an applicant to lose track of what exactly he wants to know. Apparently rankings which compare all departments of a university and have a single rank are not very useful from an applicant's perspective. Yet these are the most common rankings one can find. I know of the FT rankings which order MBA schools. It does rank B-schools in terms of research too, but clumps different branches (Accounting, Finance, Operations, etc) into one.

For other departments are there reputable and reliable portals where one can get to know rankings based on various criteria like published research, number of graduates, time taken for graduation, etc?
Are there no well-established ranking systems for academic departments? For example, these ranking systems could be similar to those in cricket or football. Such as periodic updates are made with every publication and every citation, and possibly journal reputation could also be brought into picture. In a way, would that not enhance the competitiveness in academia among similar departments?

The big difficulty with devising formal ranking systems based on numerical measures is that, outside of a handful of areas like sports, anything we can measure is at best a proxy for what we really care about.  It may start off as a pretty accurate reflection, but anyone judged on this basis will quickly discover how to manipulate it.
For example, universities in the US are often judged partially by the fraction of students they accept.  Of course, ambitious universities have adapted by advertising to encourage more applications, with no intention of accepting these applicants, but just to lower the acceptance rate by increasing the denominator.
Similarly, universities are also judged based on "yield," the fraction of admitted students who attend.  That sounds at first like a pretty good measure of popularity, but it creates an incentive to game the system by rejecting students you think are likely to choose another university in the end, and universities do just that.
Time taken to graduation can be gamed by kicking out students who are taking too long.  Employment rates can be gamed by offering ten-week temporary jobs to unemployed students, timed to coincide with the measurement of employment rate (really!).  All sorts of things can be gamed.
And this is not just a theoretical problem.  It occurs all the time in practice (if you are in the US, then your school is very likely doing some of these things), and some people are extremely upset about it.
You might think scholarly measures based on citation counts would be less subject to this, but they are not.  There are plenty of corrupt journals where editors put pressure on people to cite papers, or even use totally fraudulent methods like publishing review articles that carefully cite every paper they have recently published.  People have been caught seriously distorting their journals' impact factors by doing this, and I'm sure there are other, more clever editors who are getting away with it.  If professional success depends on influencing a number, then people will discover ways to influence it.
In summary, there's an awful tension between transparency and resistance to fraud: if you explain how your ratings work, then people will manipulate them.  Nobody has any idea how to avoid this, and the net effect is that serious scholars do not waste time trying to compile numerical rankings.  For the most part, the only people who do are those who are naive, trying to make money in unscrupulous ways, or trying to promote a cause through carefully chosen rating methods.  The rankings they produce are not worth paying attention to.
P.S.  Polls of expert opinion are generally much better than rankings based on numerical measures, but even they have their problems.  For example, the U.S. News college rankings are based partly on asking college presidents to rank other schools.  Clemson University manipulated the rankings by rating all competing schools as below average, no matter how good they were.  I suspect they weren't the only ones to do this - the amazing thing isn't that it happened, but rather that we ever found out.

Wow - I never knew things are this bad, w.r.t inflation of rankings!

@Anonymous Mathematician: Excellent answer, that was highly useful :)

http://en.wikipedia.org/wiki/Goodhart%27s_law  http://en.wikipedia.org/wiki/Campbell%27s_Law

By the way, I forgot one of my favorite examples of crazy incentives in ranking, from https://freedom-to-tinker.com/blog/felten/newsweek-fails-ap-math/.  Newsweek has ranked US high schools using the number of AP or IB exams taken divided by the number of graduating seniors.  Under this system, every time someone shows up for a exam they are unprepared for, the school's score goes up, but every time a struggling student makes it to graduation rather than dropping out, the school's score goes down.

What is the rationale for including a University's popularity among high school graduates in the ranking criteria?

@Jase: It's certainly at least somewhat problematic, since it helps turn the rankings into a popularity contest and it distorts the incentives.  I think part of the motivation is that popularity should be correlated with quality (and one might prefer to ask students what they want rather than to try to tell them).  Furthermore, popularity may actually contribute to educational quality by letting the university recruit strong students.

@AnonymousMathematician Yeah I really like your last point, good one.

Same with the Times Higher Education (THE) ranking.  I am getting spammed by my previous affiliated universities to help them provide feedback to THE.  In addition, my current universities are spamming alumni and asking their employers to provide feedback.

To answer your second question, getting accurate data can be tricky. The recent kerfuffle over the NRC rankings of computer science is a good example. The methodology was flawed, the data was old, and the data was misinterpreted, and it still took many years to produce the results !

...the data was badly sampled...

You should link to and discuss the NRC more fully. Yes, it's problematic but it warrants further explication.

I can add your list with two more well-recognized ranks:

topuniversities.com
timeshighereducation.co.uk

They indeed present some divergent results, but I guess they may provide community with some clue about the "best" universities in the world.
Indeed, I agree with you that it'd be more interesting not only check out these "marketing" ranking, that considers a bunch of aspects, sometimes not transparent (!). IMHO, a good "ranking" would depend upon your subject matter, i.e., the research of interest.
You really posed a very nice question, and I'd appreciate to hear from colleagues.

For other departments are there reputable and reliable portals where one can get to know rankings based on various criteria like published research, number of graduates, time taken for graduation, etc?

YES, in the case of computer science, for example, http://csrankings.org/#/index?all&world is a very reliable ranking that achieves precisely what you describe: a ranking of CS departments based solely on their conferences publication record, monthly updated, and with different parameters users can adjust by themselves.

The QS World ranking system report rankings by many difference subject areas. It's not equivalent to "department", but it comes close:

https://www.topuniversities.com/subject-rankings

The Leiden Ranking offers provides rankings based on a small number of very broad fields:
https://www.leidenranking.com/


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Would it hurt if I mention somewhere in my application package to a phd program that I applied to the same program?
I applied to a phd program last year and was not offered anything. This year, I would like to take a shot at that school once more. I thus wonder if it would do me good or bad or neither for me to mention somewhere in my application package that I once applied to the program? The school does not ask applicants to reveal such information in their online application system
(so that I think the present question is differentiated from this neighboring question Reapplying to same PhD program....
Suppose doing so is tacitly expected and otherwise the applicant could be considered trying to cover up something. Then what is a judicial way to describe the situation?
Moreover, could an admissions committee of a very competitive program somehow really remember who applied before and who is fresh?

I just don't see where you would mention this. If it's in the cover letter it would be a waste of space to me. Instead tell me what you have accomplished in the last year.

It's not standard, in my experience, to ask applicants if they've applied before.  (For one, this only applies to a relatively small percentage of applicants typically.)  Therefore, if they don't ask for it, they shouldn't expecting this information, and there's typically no reason to provide it.
Looking at your application, they may or may not remember you, depending on (i) if it's the same people doing admissions, (ii) how many applicants they got, and (iii) how much your application stood out.  If they don't already remember you, reminding them you were unmemorable last time won't do you many favors.
The only situation in which you might want to say something is if you were in contact with a faculty member who wanted to admit you, but for whatever reason they couldn't accept you.  In this case, you can just email that faculty member to let them know you're applying again.

Just to add another situation where mentioning the previous application might be appropriate: if a specific reason for rejection was given (say lack of publications), and that is no longer the case, it might be worth to mention that the issue was addressed. But as you mention, it very much depends on how the selection process is done and whether he was ever in touch with someone about this.


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Why are grant indirect costs so high?
I am preparing an NSF grant proposal in mathematics. I am requesting summer salary and a travel budget (and not much else), and after I compute the total I have to add an extra 50% of it and add it as the "indirect costs" of my proposed research.
This feels absurd to me (although it is the same, sometimes with an even higher rate, everywhere in the United States) -- especially since I do not require any special facilities or equipment to conduct my work. Is there a convincing argument to be made that this is reasonable?

"Special facilities or equipment" would be direct costs, not indirect costs.

Some of the answers to this question address why it's expensive to employ people, over and above their salary.  (Obviously, all the stuff about equipment and so on isn't relevant.)

You can take a more birds-eye view of the question.
Recall that the main purpose of the NSF is to support part of the public policy interests of the U.S. government. Here is a quote from "NSF at a glance":

NSF's goals--discovery, learning, research infrastructure and stewardship--provide an integrated strategy to advance the frontiers of knowledge, cultivate a world-class, broadly inclusive science and engineering workforce and expand the scientific literacy of all citizens, build the nation's research capability through investments in advanced instrumentation and facilities, and support excellence in science and engineering research and education through a capable and responsive organization.

As the NSF says on the same page,

We fulfill our mission chiefly by issuing limited-term grants -- currently about 11,000 new awards per year, with an average duration of three years -- to fund specific research proposals that have been judged the most promising by a rigorous and objective merit-review system.

It is true that indirect costs on a grant don't directly support costs of research - that's why they're "indirect costs". But they do support the national research infrastructure by passing additional funding to institutions that show merit by winning competitive grant funding. The indirect funding helps these institutions provide a research environment not only to the researchers who are awarded grants, but also to other researchers and students.
Supporting the overall national research infrastructure is certainly a reasonable part of the public policy goals of the NSF, and the indirect costs system is not the worst way I can think of to decide which institutions will receive such funding. Of course, there are also equipment grants and other specialized NSF grants, which also help support the national research capacity.

Indeed, at many universities, part of the indirect costs goes back to an investigator or department to be used freely. Moreover, most universities use these indirect funds to create internal grants (here called the central development fund) to seed new efforts or pay for research not covered by NSF, NIH, DOE, etc.

Thank you for this answer. Implicitly I had in mind that the marginal cost to the university of supporting my grant is next to nil, and was a bit annoyed to be asking the NSF to fund the university to do things it would do anyway. But you make a very good case that this is exactly the NSF's intentions.

The indirect costs help to pay for all of the other resources you have access to which are not directly paid for by other costs. For instance, these indirect costs help to pay for administrative assistants, information technology, library subscriptions, utilities, and other costs.
They can also go to pay for the costs of administrators (including the fine folks in your university grants and contracts office who actually submit your NSF proposal).
Whether or not the rate is reasonable for your university is hard to judge, but a 50% overhead rate overall is not that excessive. Compare that to industry or the US national laboratories, where the overhead rate can exceed 200%, and things don't look so bad in comparison.

Yeah I agree, I would love to have operated my business at ~50% indirect.

Is there a convincing argument to be made that this is reasonable?

One answer is no, it's not based on any real accounting.  Indirect cost rates were negotiated individually by universities in the early days of federal research funding in the U.S., and they are very difficult to change now (because many funding agencies have to coordinate on these rates).  Some universities genuinely have different costs, for example due to location, while others just negotiated more aggressively.  There's little rational basis to it, so you can't hope for a detailed breakdown that indicates exactly why it should cost this amount.
On the other hand, the indirect costs are not meant to cover just special facilities or equipment (in fact, those would be direct costs).  They are meant to cover office space, library access, computer infrastructure, administrative support, etc.  These are all rather expensive, and taking these costs into account could very plausibly increase the total by more than 50%.  So even though the numbers aren't arrived at by adding up actual costs, they really aren't crazy.

Over the years there have been repeated proposals to eliminate negotiated overhead rates and fix a single rate (of around 50%) for all institutions.  This would be tough for a few institutions that have negotiated higher rates, but it would also save an immense amount of effort that is currently going into justifying and negotiating the rates.


text:
Will withdrawing from a graduate program, affect my future admissions applications?
I am in an MS program at a big university in the US, where I pay my own tuition.
I am not happy with the quality of education I am getting at this university.
I am thinking that after this quarter is complete, that I want to officially withdraw from the program and go somewhere else. I think I can get much better education and for much less cost as well.
My question is: Will this affect me in any way for future admission to other schools? I am an A student, and I'll be withdrawing after the quarter is over, not in the middle.
Will the transcript contain some negative marker in it because I did not complete the MS program?  Has anyone been through this and found any negative effect when not completing a program?

If it is possible, you may want to consider applying to a new program while you are still in your current program.  In some sense it will be like a transfer, which may come across as a better move than to withdraw and re-apply to other schools later.
Bear in mind that you will need recommendation letters again, and you should be cultivating relationships with professors now with the hope of getting good recommendations.  While you can ask the people who wrote your last recommendation letters again, you would need to explain why you didn't get recommendations (at least one) from a professor from your current school.
If you are in the midst of fruitful research, I would also advise you to try to finish up and put together a paper for publication -- if published, this will also help in future applications, and you don't want to waste the effort if you can help it.
One further caveat: graduate schools sometimes have a cap on how many courses you can transfer from a previous school, and you may find that you have to re-take a number of courses you've already passed (and paid for).  The financial benefit from withdrawing now may not be as good as you hope.

Your transcript will very likely have a notation that shows you withdrew from the program; to claim that you are still enrolled when you are not would be dishonest (if either you or the university said so!).
And yes, this will be something that you will need to explain to schools to which you apply in the future. Just saying "it's not good enough for me" is a bad reason to withdraw from the program, because it suggests a "diva-like" attitude that is not particularly desirable (in just about any circumstances). If you're responsible for paying your tuition, and found you could no longer afford it, that would be a more tolerable reason.
But you will need to explain this, and it can definitely have an impact on the decision of future admissions committees.


text:
How can I find the DOI for an old mathematical paper which is not in English?
(Not sure if this is the right SX site, but math.sx seemed to have no questions concerning DOIs.)
Everything I cite in my thesis has a DOI or URL (I think that's important), but I'm citing an article that was the first to mention a kind of problem,

Arkadi Nemirovski. Nonparametric estimation of smooth regression
  functions. In: Tekhnicheskaya Kibernetika 3 (1985)

which seems to be quite obscure, it's not even listed on the author's website. It's not in our library (or any catalog I searched), but just a handed-down copy of unknown origin.
The journal doesn't seem to exist any more (or it doesn't have a website), and crossref.org yields nothing. The article is translated, there are some inconsistencies with transliteration, i.e. the author's last name is sometimes written Nemirovskiĭ, the journal is sometimes written as Techničeskaja, the title might be completely different, etc.
Any pointers where I could find some canonical information?

The full name is Izvestiya Akademii Nauk SSSR, Tekhnicheskaya Kibernetika. As you inferred, it looks like it was terminated, doesn't have a web site, and all that was before the advent of Digital Object Identifiers. So, what are you asking for exactly?

Everything I cite in my thesis has a DOI or URL — As a fellow sufferer of bibliographic OCD, I understand your frustration, but as you've just discovered, not every citeable object has a DOI or URL. Not even close.  Move on with your life.

If you want truly canonical information, you can ask a librarian for help in getting a copy of the original paper by interlibrary loan.  You could also write to Nemirovski for more information (people are often flattered when someone expresses interest in one of their more obscure publications).

Everything I cite in my thesis has a DOI or URL (I think that's important). I think this is a shame. What about all the wonderful literature that predates DOI and doesn't have one?

As others have said, not every (old) article has a DOI or a URL. However, in mathematics every article since 1940 has an MR number which uniquely identifies it. So go to mathscinet and look up this article. I just did, it has MR number MR0844292. The bibliographical information on mathscinet (like the transliteration of the author's name) would also be considered the "canonical information".

Awesome! Thanks, I didn't even know that database.

Short answer: The full name is Izvestiya Akademii Nauk SSSR, Tekhnicheskaya Kibernetika. As you inferred, it looks like it was terminated, doesn't have a web site, and all that was before the advent of Digital Object Identifiers. So, what are you asking for exactly?

Obviously, there is a longer answer to that question. As you said, it is unfortunate this content doesn't have a canonical URL, or even a Digital Object Identifier. The good news is that you can actually fix that problem!

Create and incorporate your own company: Lost and Inaccessible Academic Content, Inc. (actual title may vary). Depending on local legislation, this might not be so hard as it sounds.
Contact a DOI Registration Agency to register a DOI prefix.
Register the DOI name and associated metadata.
Write down that DOI name in your thesis bibliography.
Bathe in the joy of the world now being a (slightly) more organized (and thus better) place.

my question was phrased a bit too restrictive, I was looking for any kind of canonical identifier, the MR number from Marcus' answer is good enough for me.


text:
Is it legal to run interviews for an academic job when the post has already being assigned?
The normal UK process to hire new academic staff would be:

The position is placed on job adverts, websites, specialized magazines
The curricula and forms from prospective candidates are collected
A filter is applied and a short-list produced
The short-list candidates sit in a workbench for an interview
The position is assigned to the most qualified candidate

I happen to know of a case where the position is already assigned, but the job avert has been published, so it should be open to all candidates. Since the position has already been assigned, steps 2 through 4 are a waste of time and paperwork as other responding candidates will not be seriously considered.
Is this superfluous search process legal?

How conclusively do you mean "already assigned"?  There could be a big difference between several cases: an intent to hire a specific person no matter how the applications/interviews go, an intent to hire someone with a willingness to hire someone else instead if a better candidate appears, an offer already made to a candidate with interviews to select a backup in case the offer is turned down, an offer already made and accepted with a possibility of a second offer for an extraordinary candidate, or an offer already made and accepted with no possibility of further offers.

the job specification, type and spectrum of requested skills are pointing towards one SPECIFIC person, who will be appointed. Friendships and past comraderie also play a part.

In many situations it's actually NOT legal to go ahead and hire someone without advertising and/or interviewing candidates. Pretty common in government-funded institutions (not just Universities either). Seems pretty uncommon for them to interview many people if they already have a top choice and the ad's gone out though.

@Irwin, with a little bit of expansion, your comment (with some of Anonymous Mathematician's) becomes a good answer to this question.

This is by no means just a UK thing. Similar processes exist in the US and, I suspect, in many other places.

@BenjaminMakoHill: I am not naive, guys, I know that these things happen... My question is "is this legal?" If this is not legal, it should be reported to the media, the authorities, whomever. At the very least I could easily win a bet on Paddy Clarke :)

I was suggesting that the process/routine/legal requirements you describe are common in the US. Of course, the practice of ignoring it probably is common as well. That said, I think @Silvado answered this well. The difference between legal and illegal proving people's intent. That's going to be extremely difficult always and frequently impossible.

In many cases, academic institutions will be legally obliged to fill positions according to the procedure you described. This usually requires publishing a call for applications in a suitable medium, and putting together a short list of selected candidates based on qualification for the position and fit to the announcement.
Now there may be the "problem" that the person or group that will select the candidate already has a specific candidate in mind and want to "assign" the position to that candidate. However, simply hiring that candidate without going through the formal process would in fact be illegal. So the typical workaround in this case is to make the announcement so specific that the desired candidate will be the best qualified person for the position. It may be ethically questionable, but I fear it is totally legal.
Still, even for other candidates, this approach seems to be better than allowing the institution to just fill the position without the formal process. Especially if there is a committee deciding on the short list, this may even be different from the group that made up the announcement, and there may be people pushing for candidates they deem more qualified than the originally desired candidate. Chances for other candidates will clearly be rather low, but still higher than zero as in the case without announcement.
As to the question whether it is possible to find out about such a situation in advance, I fear it is not that easy. It works best when one has good contacts to people in the committee, and can ask informally about the situation. Otherwise, a reasonable approach would be to phone a contact given in the announcement and discuss details of the position. In many cases, one should be able to figure out whether the other person is open to applications or not.

Another clue is an overly specific description of the position and the required research area.

@FedericoPoloni: that's a good hint, and it what started the question altogether.

I have seen a few cases where a very specific position was announced with a very specific candidate in mind, but after the legally mandated search process, someone else got the offer.

In the private sector/industry this is so common that a regular piece of job hunting advice is "if it is published in the paper or on a big job site, the job is already filled." I once even had a recruiter outright tell me I was only called in because the company required at least X amount of interviews (least pleasant interview ever). However, as @JeffE noted, I've also personally observed a few cases of an heir apparent passed over in favor of an outside candidate. Its an unpleasant, though not uncommon, reality of the workplace.


text:
Can I simultaneously pursue separate masters and PhD degrees?
Can I enroll in a masters degree program via correspondence at another university while simultaneously enrolled as PhD as a regular student from University of Delhi?

Could you elaborate as to why you want to do that?

In 2 different fields?

Why don't you ask the University of Delhi?  They are the only ones who could give you a definitive answer.

Are either funded by anyone, and if so who?

@shan23 - This would make sense for someone wanting to pursue a PhD in their field of interest in a university while simultaneously pursuing an MBA or other more business-oriented degree elsewhere.

The answer to the question as stated is almost certainly "yes". A correspondence degree can be pursued by anyone, regardless of occupation, and your occupation as a PhD student shouldn't affect that. Note that your department may discourage this practice, as you would effectively be holding two full-time jobs (or one full-time and one part-time, depending on how quickly you pursue the correspondence degree).

I agree if the two degrees are sufficiently distinct, but the closer they get the more problems there could be.  A PhD and an MBA should be OK, as you mention above, sounds plausible.

I think most departments set the maximum number of hours you can work an outside job. In this case I think pursuing a second degree would count as a job. Funding agencies have even tighter rules. If you are being funded for both degrees, that would also cause major problems. Finally, most advisors would frown upon this.


text:
conflicted whether to transfer or not
I am a college sophomore and I am debating transferring out of my current school, Hunter college. My GPA is 3.56 and I am a CS and psychology major, concentration of behavioral neuroscience.
Now, I have always been interested in research but the resources in my school seems very tight and my overall experience has been very unsatisfying. My ultimate goal is to try out for MD/PhD program with a background in BCI (Brain computer interface) but my school offers no program in any close proximation.
So, should I transfer out or hold on until the end of my 4 years? And also is my GPA reasonable to transfer into better schools like NYU or WakeForest University?
Should I focus on graduating from my current school or plan to transfer to a more prestigious school?

If your goal is MD/Ph.D, your PreMed GPA is likely to matter more than your comprehensive GPA.  What is it?

By premed GPA do you mean the gpa of all the classes required for medschool? Or each individual course?

Yes, the average of all of your medschool requirements without the other poetry, anthropology, whatever else you're taking.

I am not an expert in neuroscience or BCI. However, I found BP-Endure program where your current school Hunter College is a major partner.
On their web page,

During the academic year students will work with a research mentor at Hunter or NYU and during the summer in one of the partnering institutions. The BP-ENDURE program selects students from both Hunter College and NYU to participate. Hunter students will receive funding in the form of tuition remission and a stipend during the academic year and will also receive summer funding.

I am not sure why you said the resources in my school seems very tight and my school offers no program in any close proximation. Are you having difficulty getting into that program?
Transferring to another school may cost you a lot than what you'll gain. You may lose the credits you already have and retake courses you have taken plus your financial loss. However, if you have other difficulties with your current school(which you have not mentioned), then transferring may be an option for you.
My advice for you specifically, stay there and study hard, grab any opportunity to enter into the BP-Endure program.
In general, however, if your research area requires resources you don't have in your current school, it's worth considering transferring. You need to weigh on the cost vs. gain. You can either stay in the current school acquiring fundamental knowledge and apply to a graduate school where you would have better resources after you graduate, or transfer to another undergraduate school with much better resources.

I transferred schools during undergraduate under a similar situation, but with a different academic focus. The school I ended up transferring into was far more competitive, so I got what I wanted.
Unfortunately, I also ended up staying in the program for an additional year because the school I transferred into required that I take their version of the same courses.
When I finally graduated, I was proud that I was pushed harder and learned more, but found that many of the same opportunities existed despite having gone to a better university.
I have since completed a masters without any intentions of continuing towards a PhD, but I found that I do enjoy research, so now I am in the second year of my PhD studies. Actually, I regret having entered into the PhD program but that is beside the point.
The lessons that I've learned from about 8 years of college at this point are that undergraduate research appointments are... well... not all they're cracked up to be.
The better research opportunities are available for masters students, and the best for PhD students, and even that is a completely relative situation depending on a huge number of factors. I've seen two of my fellow PhD students transfer universities after their professor took a job elsewhere. I've seen PhD students in very competitive departments get stuck with a lame professor; and I've likewise seen PhD students in lame departments find an awesome professor.
And, to make research opportunities more difficult to gauge: its commonly known amongst graduate students that the pecking order for research appointments benefits the PhDs the most, and the undergraduates the least. Often the undergraduates are used for all the crap nobody else wants to do, and while learning the basics might be good for an undergraduate, the work is usually tedious, boring and repetitive.
Masters students are usually given more application based work, which is really good for honing skills, and the PhDs are given the more theoretical work, which even then can be a professors sloppy seconds.
The best advice I can give you is to stay exactly where you and look for research opportunities with a professor that you really enjoy and want for mentorship. If you have a particular project in mind, then do an independent study with them. Having a solid GPA and having demonstrated an individual drive can speak volumes more than attaching yourself to a bunch of names (though I don't underestimate the name attachment in academia).
EDIT: As a second thought, I can't tell you how much it sucked switching universities and becoming distant with those friendships I made. Yeah, I made new friends that were also really awesome, but starting over can be lonely.

-1 because this answer is overly personal, rambling

Yes it's personal, it's first hand experience for having gone thorough what the OP asked about. Rambling? It is a bit long, but I didn't want to write something generic like "there is no right or wrong answer".

This forum, like StackExchange sites in general, is not a chat room. This site's instructions make this clear, and emphasize that personal opinion and chit-chat are not valued highly. While my answer includes opinion, it's voiced in a general way and it represents norms of academic assessment.

Pot, meet kettle.

It's all about what you accomplish - whether you stay where you are or transfer. Yes, if you can transfer to a school with a stronger reputation and hit the ground running, that may put you in a better position. That said, it's not going to be easy to transfer in with only a fairly high GPA at a less-rigorous school, and you'll lose some time in making the transition/adjusting.
A transfer can be a warning sign - is this someone with a pattern of not finishing what they start, or was this an isolated, carefully-considered, strategic choice? If the latter, no problem.
When I consider applicants, what they do (e.g. specific field) is far less important than how they advance and accomplish, what aptitude they have demonstrated for gaining new skills and working with a team. I'm sure there are things that could be accomplished at your current school, even if the topic is not your first choice. The letters from mentors carry a lot of weight. It takes time to establish strong relationships after a transfer - keep that in mind if you already have an advocate on the faculty at your current school (and consider getting their advice on this).
There is no right or wrong decision; regardless of whether you stay or go, the real challenge is making the most of the available resources and developing strong mentors among the faculty.

Well your GPA seems very good and i feel you can get admission in any other college. If you think you are not satisfied with the performance of your institute then there is no point of staying there because at the back of your mind you will always be thinking that you could have been to some better place. I believe that you should have been more cautious before choosing your institute because switching it is a bit difficult task. If you would have assured before admission that an institute is accredited as per standards, http://www.iao.org/iao/institutional-accreditation/, then you would have an enhanced sense of credibility. My advice is to look for another institute which you feel is as per global standards.

Don't transfer. Try to learn to make use of the available resources. Focus on hard work and your own research. Sometimes studying a difficult book is more rewarding than having access to high-tech instruments and possibly not really understanding how they work.

If he transfers, he still can study difficult books with access to high-tech instruments. Your reasoning is not convincing.

But the post also may suggest it might be easier for the student to obtain more knowledge just because there are more high-tech instruments available. In my opinion, it's not usually the case because most students lack in-depth knowledge of the basic instruments, not to mention high-tech instruments.

Where did the OP mention high-tech instruments? He says the resources in my school seems very tight. You're the one who interpretes that means access to high-tech instruments !

The student's description is self-explanatory. Not every university can afford high-tech Brain computer interface instruments (I did a lot of research on that and they are very costly, even for college).


text:
Is it appropriate and useful to inquire if an open position has an internal candidate?
It is not unusual for institutes to advertise positions (faculty or not) for which there is an internal candidate.  In such situations, for external candidates, it may be difficult if not impossible to get in.  When a position is advertised, is it appropriate and useful to inquire if a position has an internal candidate already?  It might save a lot of time for the external candidate and possibly others (such as recommendation-letter-writers).

The question you didn't ask, but that everyone seems to want to answer, is "Short of directly asking, are there other ways to tell?"

It's always appropriate to ask, as long you're careful not to suggest that internal and external candidates are being treated differently.  But by far the most likely (and most appropriate) answer is "We can't tell you."  So, no, it's not useful.

I assume that there are often-if-not-always internal candidates for open positions, in academia and outside. There are always students looking for Ph.D. slots, Ph.D. students looking for postdoc positions, assistant and associate professors looking to move up to the next level. (Same for non-faculty positions, but that seems OT.) Sometimes the people responsible for the position may not even know yet about such internal candidates, because they may not yet have sent in their application.
So the question probably rather is whether these internal candidates are already frontrunners. The professor may want his extremely productive Ph.D. student to continue in the postdoc slot but may need to advertise externally for some procedural reason. The department may want to continue a certain research specialization and plan on promoting the retiring professor's assistant prof. In such a situation, external candidates will need to be very convincing to win.
But: how often will the external candidate be told this? If the external advertisement is legally required, the hiring people may even open themselves up to litigation if they openly tell an applicant that they are only soliciting outside applications as a fig leaf.
On the other hand, the department may explicitly be searching for "new blood", so internal candidates may actually have worse chances than external ones. Which, again, nobody will tell you (or the internal candidate).
Of course, it makes sense to tap your network and see whether the grapevine can tell you more than official channels. However, this kind of information can be unreliable. So if you hear from multiple sources that a given position will be filled internally, it may make sense to not make the effort.
Thus: there will likely be internal candidates, but you will probably not know how good their chances are. If you are a good match for the position, go and apply. Don't worry about internal candidates. This is one part of the hiring situation you can't control, just like the mood of your interviewers. Giving up on an application because there is an internal candidate will be counterproductive in the long run.

"the hiring people may even open themselves up to litigation if they openly tell an applicant that they are only soliciting outside applications as a fig leaf" -- they might open themselves to litigation just by doing it, depending who (if anyone) audits their processes. But sure it's even worse if the person directly harmed by your law-breaking knows that you're breaking the law!

This answer hits the nail fully on the head.  I will also quote the key passage: "But: how often will the external candidate be told this? If the external advertisement is legally required, the hiring people may even open themselves up to litigation if they openly tell an applicant that they are only soliciting outside applications as a fig leaf."  Right: this is why it would be pointless and perhaps even inappropriate to formally ask about this.  Inquiring openly whether someone is up to skullduggery is liable to get a negative reaction whether they are or not!

I think it is only really useful if you know somebody at your target institution personally and are able to inquire "off the records". Formally asking a stranger whether an application procedure is just for show seems pointless - as Stephen says, the only realistic answer will be No, of course not.
However, note that your connection does not necessarily need to be somebody on the hiring committee. Oftentimes, it is enough to know another PhD student, who can then open his ears a bit for you. If there already is an internal "favorite" for a given position, this is often not really a secret internally. For instance, I have seen a case where, when the contract of a highly distinguished postdoc ended, a call for a assistant professor appeared out of thin air with a scope that looked as if it was copied and pasted (which it might actually have been) from the postdocs research website. From the outside, this might not have been insanely obvious, but internally, everybody knew who will be hired for this position.

It's usually a good idea to make some informal contact with the person offering the job before you submit an application. Send an email to briefly introduce yourself and maybe ask some questions (are there teaching opportunities for example). I've heard of cases where there will be a delayed or curt reply which may indicate that they're not interested in you. On the other hand if someone is genuinely looking for someone they are more likely to reply promptly and positively.

I would be careful about reading too much into the promptness of an answer, especially in an academic context. These people have a lot of other things to do, unlike an HR rep in industry, so some tardiness and curtness could simple be a consequence of the latest grant round/paper revision/manuscript review/student difficulty/interminable committee meeting...


text:
To pursue research career in physics; How much physics courses should I pass in my undergraduate engineering degree?
I am an undergraduate student of electronics and telecommunication engineering in a govt. college in India. But I am extremely interested in physics and mathematics. I want to pursue a research career in physics and mathematics. I generally receive suggestions like taking the GRE test. But I have the following questions:

What is the minimum amount of physics I am supposed to have mastered at the end of my engineering?
How much of physics or physics related subjects should I have in my UG course?
How much is an adequate grade (What puzzles me most is that if I am intending to do physics why should my grades in engineering should be considered?)

I am only familiar with the US system, but I encourage you to check with a prospective department/university in your program area. If you want to transfer to undergrad, there are usually specific "transcript review" policies to see what credits can transfer/count towards your new degree. If you are seeking grad school acceptance in physics after completing a UG in engineering, that is more heavily dependent on what each school states in their entrance requirements. I'm looking at engineering from a non-engineering degree, and one school only required 3 engnr and no physics classes at all. YMMV

As to grades, this also varies widely by school. In the US some grad schools only consider the last 2 years of work towards the GPA, some have one requirement for major courses and a different one for non-major courses (so say 3.5 average for major but only 2.5 for others), and for most they require a relatively low entrance requirement but prefer higher grades. As to reasoning for considering all grades, institutions often reasonably worry that if you average C's and D's in areas you don't like that perhaps you'll also do poorly when faced with a required course/task you don't like.

@user7014 You should try getting into a good masters program in India itself before going phd abroad. Read my full answer below.

There are plenty of options in India for an engineer to enter physics field. Most of them are mentioned in this  blog http://physicsafterengineering.blogspot.in

Cross-disciplinary movement does happen fairly frequently, particularly between engineering and the mathematical and physical sciences. Unfortunately, as the academic disciplines themselves become more cross-disciplinary, it becomes much harder to say what specific training one needs to move from one field to another between the undergraduate and graduate levels.
A good way to check for the qualifications you are likely to need is to examine the course requirements of schools you're already interested in attending as a graduate student—if your undergraduate program has sufficient depth in math and physics to allow you to take those courses as a graduate student, then an admissions committee will likely be OK with the lateral movement.
If you have questions about what is necessary, you can contact the person in charge of admissions at some of the departments you're interested in for further clarification.

Could you add something on grades ?

About all I can say with respect to grades is do the best job you can. There's no single magic score," but the better you do, obviously, the better your overall chances.

It is very difficult, almost impossible, to enter into a good graduate program in the US with an undergraduate program in engineering from India. So, instead of preparing for the GRE, you should try to get into the Masters program in Math at
ISI, CMI or maybe at the IIT's. If you're interested in physics you should try to get into a Masters physics program at IIT through JAM. So, you should start preparing for their entrance tests.
I would suggest you to choose either physics or math because preparing for both the entrance tests at the same time can be really difficult.
Grades
Since you asked about grades and courses I think these pages will give you a good idea.
http://www.physicsgre.com/viewtopic.php?f=3&t=1847
http://www.mathematicsgre.com/viewtopic.php?f=1&t=1003
http://www.mathematicsgre.com/viewtopic.php?f=1&t=685

I am on the same path as of yours. I am thinking of taking IELTS test. Well actually I did Electronics and Comm bachelors and worked for 2 years in embedded systems and now planning for physics masters.To bridge the gap, I am right now taking courses in coursera.org and edx.org. Perhaps you can consider this too.

I believe Engineering (communication) gives you a good amount of mathematical tools. It gives you basics in Physics like electromagnetic for instance. In Physics and Math, they concentrate more on the physical aspects and mathematical aspects of Physics and Math. In engineering, they focus more on applications. Moreover, they focus much more on theoretical aspects. For instance, there is a big difference between a probability course for mathematicians and that for communication engineers.
I think you can compete, since engineering students are usually smart. Perhaps you will need to take few courses before being able to compete with students having undergrad degrees in Physics or even Math.
Note: I have an engineering degree (electrical), and then moved to Computer science. I can't really answer your question precisely. But when I started my Master I needed to do study 2-4 CS courses.

Well , I actually intend to do masters in physics or maths first before moving up to grad school. Could you add something on grades  and I hope masters degree is a fine way to fulfill the requirements of some grad school.

Well. I dont know how they will count your degree. They will usually send your grades to a committee that will decide which courses will fit in the new program and which won't. Your GPA, sadly, is the main measure university take before considering students in any study field.

The amount of math in engineering is not at all enough for doing graduate work in mathematics. To have a non-zero chance of getting of getting into a decent grad school(phd) in US the minimum bare requirement is courses in abstract algebra, real analysis, complex analysis and point-set topology. But students who do get selected have actually taken many advanced(graduate level) courses during their undergraduate years


text:
Are there standard example research papers for teaching methodology and experiments?
Are there recommended or standard published papers (not books) that show great research methodology/ scientific methods?  I am trying to help out a friend who is in business and they are trying to study aspects of humans (in terms of their clients).  I gave him the book The Craft of Research, but it's long and I wonder if there is a paper that could do the same job.  Basically I want to show him a good example of coming up with a hypothesis, accounting for variables (such as stating that something was done in order to eliminate a problem), and analyzing the results.

If he is in business and he can't even finish The Craft of Research, I'd rather suggest him budget some consultant money to hire someone (maybe you?) to work with him through the process. Learning and immediately applying research hastily would likely waste time and resources. It's correct that some papers may introduce some 101s about research design and analysis, but papers tend to be concise and use citation extensively; he may still end up needing to reference other publications and articles.

I know you didn't ask for books, but my answer may be helpful to you (and others). My PhD methodology is Design Science.  An excellent academic scholarly book, is "Design Science Methodology", by Wieringa, Springer, 2014.  There are about 100 references, in the book.  So you can learn from the book, and then find the relevance published papers that you are looking for.

Qulatrics has a nice concise (and free) guide to doing marketing research. Not a journal article, but I give it to my students in my research methods course because it's practical and comprehensive but not overwhelming. In fact, they have a lot of useful resources here: http://www.qualtrics.com/university/researchsuite/research-resources/other-resources/ebook-downloads/

I personally find a lot of both elegance and accessibility in the descriptions of well-done infant and animal cognition studies.  A nice source for examples is the Harvard Laboratory for Developmental Studies, and a nice short accessible piece from their library is this one: "Chicks, like children, spontaneously reorient by three-dimensional environmental geometry, not by image matching": it's only 3 pages long, presents the hypothesis, method, and results quite tersely, and the experimental apparatus can be built with common household objects.


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How important is advisor's supervision for a Ph.D. student to be an independent researcher?
I have seen one extreme of the spectrum, where a person conducts great research without even attending college. For a student to become an independent researcher, how much is on the advisor's shoulder and how much on the student? I know the answers may be all over the map. Just curious what your takes are on this question. Anecdotes and personal examples are welcome.
I have noticed some professors are more successful in supervising students to become independent researchers (approximated by the number/ratio of alumni who land research jobs) than others, even though their research portfolios and student qualities are similar (e.g., in the same department). That's one reason I bring up this question.

This isn't a discussion forum; invitations for "your takes on this question" where "anecdotes and personal examples are welcome" are a red flag that this is not the right place to ask this question. It's too broad (there are too many possible "right-ish" answers), and it's opinion-based.

Questions asking for opinions or anecdotes are discouraged on this site.

I agree with the comments but think that there may be a good (and on-topic) question close at hand.  If the question were e.g. "How can an advisor best guide a student to becoming an independent researcher?" then I would be very interested in the answers (even though they would probably constitute various answers "takes on this question" and would be enriched by the inclusion of "anecdotes and personal examples"!).

@EnergyNumbers So do you suggest I revise my question to be more specific and remove hints of discussion and/or opinion, or I submit a new question somewhere else? And where should it be?

There are two major types of advisor approaches which I've encountered during my studies:

Hands-off, abstract guidance only. Hint at which areas are interesting or currently active, but do not throw yourself into your student's work. Usually such advisors will gladly proofread the student's work for errors, but they rarely know what to do if a student gets seriously stuck. Advisor sessions may be spent discussing current trends, future work of either the advisor or the student or, in some cases, simply "life advice".
Co-worker approach. The advisor treats his student as an equal and tries to immerse himself into the student's work (or vice versa). By having a lot of exposure to the advisor's routine (how he goes around solving problems, how much time he spends doing research, how he prepares for lectures, etc.), the teacher aims to guide the student by example.

These two approaches are often seen in combination (while the student may be treated as a coworker, he still is usually the one to do the typesetting, the programming, and other time-consuming tasks).
Personally, I prefer the second approach, which is likely because I am not that settled in the "theoretical research" routine. Some of my friends, who have known since their Master's studies what they want to do, are very enthusiastic about having a well known professor with the hands-off approach.
To answer the question about either approach fostering independence, I believe the hands-off approach leads to much larger independence as a researcher, but the coworker approach may lead to a much better work ethic (mirroring the professor), which is tremendously important in science.
It seems to me that students have a harder time successfully completing research (asking the right question, having the right insights, etc.) than being independent. Therefore I believe that student/advisor relationship does not need to promote "independence" in any substantial way.

Pairing students and advisers with complementary goals, needs, and expectations is the key.  If a student is already self-motivated, capable, independent, and has a fully-funded, well-conceived research project, then they can be paired with an adviser who gives little oversight.  However, if a student is lacking in one or more of those areas, then they should be paired with an adviser who can support them and help them improve on their weaker skills.
References
Delany, D. "A Review of the Literature on Effective PhD Supervision" Centre for Academic Practice and Student Learning, Trinity College (2008).
Zhao, F. "Postgraduate Research Supervision: A Process of Knowledge Management." (2001)

I don't see how could this adequately answer the question.


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Where can I find templates for a mathematics research paper?
I've recently typed up a mathematics research paper, but I would like to make it appear more formal when I submit it to be peer-reviewed.
Also, how would I be able to incorporate LATEX into my paper?
Are there any templates out there that follow formats similar (maybe even exact) to examples such as this and this one.

The two links you gave both provide the LaTeX source, if you just delete the pdf file name from the URL: http://www.ams.jhu.edu/~ers/learn-latex/ and http://www.math.umbc.edu/~gobbert/latex/

You can download the latex sources of the vast majority of (actually almost all) math preprints posted to arXiv. Just go to the abstract page of your favorite math paper and click on "Other formats" under "Download." There you can find the link to the source file in latex as long as the author(s) uploaded it and complied by arXiv's latex engine (which pretty much everyone does).
I think reading the actual sources of nicely typeset papers you like is a very effective way to learn how to latex.
For example, here's the abstract page of my latest preprint:
http://arxiv.org/abs/1409.2559
and its source is here:
http://arxiv.org/format/1409.2559v4
To get the latex file I submitted, click "Download source" near the bottom right.
The file is in compressed format. But as the arXiv page says, your browser may uncompress the file. My Google Chrome for Mac does this, so what I actually get by clicking the download link is a latex file, which is named "1409.2559v4" with no extension. If your browser behaves the same way, you can simply rename the file to attach ".tex" at the end if the extension is important.

The question is based on something of a misunderstanding. On Stack Exchange, it is possible to incorporate LaTeX into a post by using dollar signs. However, when you're writing a stand-alone document, you don't "incorporate" LaTeX: rather, you write the whole document in LaTeX.  (An analogy would be asking "How do I incorporate MS Word into a document?" You dont – you write the whole document that way.)
As such, you'll have to re-typeset the whole document using LaTeX, if that's the route you want to go down.  The good news is that a LaTeX document looks a lot like a Stack Exchange post when you're editing it. It's mostly just a text file, with ordinary text as text and mathematics in dollar signs.  (Plus a "preamble" of initialization commands at the top, and a few commands within the document, such as to start a new section.)  So you can mostly copy-paste from your Word document (or whatever it is you used for the first version), put dollar signs around short pieces of maths that appear in the main text (e.g., Pythagoras proved that $a^2+b^2=c^2$.) You will have to re-work the displayed equations and any more complex pieces of inline mathematics.

I would recommend using the amsart LaTeX format: http://www.ctan.org/pkg/amsart
If you would like an intro to LaTeX itself, consider going through the wikibook: http://en.m.wikibooks.org/wiki/LaTeX

Often, the journal you want to submit to will provide a LaTeX template. Look at its "Guide for Authors" section.


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Should I provide references to a function which is used as part of a programming language?
I am writing a paper, which in the application used a function from a programming language (in this case, it is OpenCV function canny edge detection).  When is or is not appropriate to explain the algorithm in mathematics/words and when or how should a function be referenced.
In this case, OpenCV explains the algorithm http://docs.opencv.org/doc/tutorials/imgproc/imgtrans/canny_detector/canny_detector.html
Should I just provide a link to this, as I did not modify the algorithm but it is an important part of the implementation decision.
Is there a standard way of deciding to reference the language, function, or original algorithm?

In this case I would opt to cite the paper in which Canny edge detection was introduced. Citing OpenCV as a whole is more appropriate than referring to a specific function, e.g. "we obtained our results using OpenCV [Bradski00]". Since you use OpenCV, you should also cite the related paper.
I would only refer to a specific function in a software package if it does not implement a known algorithm and therefore requires special attention.

I addition the guys at OpenCV suggest http://code.opencv.org/projects/opencv/wiki/CiteOpenCV

A particular function may matter (they may be more more ways to do it within a given package, implementation may matter (from numerical precision, through technical parameters and details, to possible bugs)).

Sometimes I see a reference to a particular function in a given library, and I consider it a great practice.
If the problem has various algorithms, or algorithms have various implementations (differing by technical details, numerical precision, etc) explicitly mentioning package will help the reader. I don't see a reason to conceal it.
For me:

BAD: "We performed edge detection." (How? Magic!).
OK: "We obtained our results using OpenCV [Bradski00]" (There may be more ways to do it, so happy guessing game for anyone trying to reimplement this.)
BETTER: "We performed edge detection with canny from OpenCV package [cit], which implements algorithm_name [cit]."
BEST: "We performed edge detection with canny from OpenCV package [cit], which implements algorithm_name [cit]. Full code is available at http://..."


text:
How to make a paper's author willing to help me with his source code like a semi-supervisor?
I am really in trouble. I am doing my MA thesis on wireless sensor networks, and I have a source code with more than 16 files and each one more than 5000 lines. It's very complex and has no documentation and that source code is all I have to do my thesis.
I am totally dependent on the author's help. I have been working on his code for almost three months now but because of the lack of documentation, my progress is very very slow. Also, my supervisor has no knowledge of the concept or the source code, and I have no time to change the supervisor, concept or source code.
So, how I can tell the author of the code please help me? How can I make him willing to help? What should I tell him in the emails?
By the way, he answered my questions in the past. I asked three questions and he answered them. I've previously asked about the etiquette of repeated emails to him in this question.
But I need his help like semi-supervisor. By the way he is a kind person as far as I know.

"I asked three questions and he answered them. But I need his help like semi-supervisor." I really think you are asking for / expecting too much.

This question is presumably related to your previous question, "What is the etiquette for repeatedly emailing questions to an author whose work I'm building on?" Did you follow the advice given in an answer you've already accepted there?

I can't talk for others, but in order to make me willing to help you to the level that I suspect you want the paper's author to help you, you would have to pay me a substantial amount of money.

If  you are doing something non-trivial on top of the original paper, you can suggest a collaboration, with the goal of eventually writing a paper together. But that would only work if you are bringing enough to the table.

If you are indeed "totally dependent upon the author's help", you are doing the wrong project.


text:
What are the ethics of getting help from online forums?
As an engineer, sometimes in my research I come across a mathematical problem that either is beyond my mathematical skills, or I know that someone, somewhere must have seen something like it before and can point me in the right direction, hence saving me time.
Asking on math.stackexchange often does the trick, but I wonder what the ethics involved are. For instance, if someone provides a complete answer, and the result turns out to be integral to the paper, should I offer them authorship?
PS: I'm not talking about a result that is novel in itself - i.e. it would not be considered as a contribution to mathematics. The result will be an application of standard mathematics to a particular engineering problem.

possible duplicate of How to acknowledge ideas/clue/discussions on StackExchange?

I think the question is somewhat misleadingly worded. You are not really asking about the ethics of getting help. In most contexts, you can unquestionably ask others for help. You're asking about the ethical requirements of what obligations that help creates on you in terms of later use.

Do not be afraid of giving people co-authorship if they contributed to your work. It doesn't hurt you (really) and it helps someone who helped you.

Asking on math.stackexchange often does the trick, but I wonder what the ethics involved are. For instance, if someone provides a complete answer, and the result turns out to be integral to the paper, should I offer them authorship?

If someone else made an integral contribution to your work, it seems appropriate to offer them coauthorship, yes.  You go on to say:

I'm not talking about a result that is novel in itself - i.e. it would not be considered as a contribution to mathematics. The result will be an application of standard mathematics to a particular engineering problem.

I see what you're getting at, but still: if you did not have the knowledge to write the paper, then asked someone for help, then based on their help you can write the paper, then it seems that they deserve to be offered coauthorship even if what they provided was from the perspective of their discipline completely routine and well-known.
One example that springs to mind is the Hardy-Weinberg Principle: this is a famous (and, in my understanding, rather important) law of genetics whose mathematical content really does seem to amount to: if p+q = 1, then p^2+2pq + q^2 = 1.  The history of this is not what I had assumed it to be: it is not a collaboration between Hardy and Weinberg (Weinberg was a German physician who had independently discovered the law at about the same time).  Rather Reginald Punnett was having trouble defending Mendelian genetics against an argument of Udny Yule that dominant alleles would weed out recessive ones and thus genotypic frequencies would not remain stable in the population.  Punnett brought this up to (the great analytic number theorist) G.H. Hardy who happened to be his cricket partner, who duly submitted a letter to the journal Science.  As the wikipedia article points out, Hardy makes his take on his "contribution" pretty clear, e.g. in the phrasing "a little mathematics of the multiplication-table type is enough to show...."  It is interesting that this is not called the "Hardy-Punnett Law" (though there are Punnett squares, which seem to my inexpert eye to be pretty much the same thing).  One striking thing about this example is that the mathematics here is really trivial: it is hard to imagine any mathematician (or engineer, etc.) who would not have been able to answer the question.
Of course, just because you offer someone coauthorship does not mean that they will take it.  Most mathematicians I know are not interested in being coauthors of papers in other disciplines for which their contribution was purely mathematical and is regarded by them as "trivial", "well-known" or both.  If someone declines coauthorship then it seems largely agreed upon that you can go on to write the paper by yourself and include a clear acknowledgement of their contribution.


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Should I pick a time if a professor asks me to?
When a professor gives me some timelines to choose for an interview, I always say I am available anytime that suits your schedule, mainly because all times are OK with me, I can even have a discussion even at work.
Do you think its better to pick a timeline rather than saying you are OK with any time?

If the professor asks you to pick a time, then the most likely explanation for that is that the professor wants you to pick a time.  The same applies to doctors, dentists, lawyers, or anyone else you might want to make an appointment with.

Sorry for the snarkiness, but this would be a great contender on "So you THINK you can OVERTHINK?!"

Why are you hesitant to pick one when given a list of options? Let's flip the table: if you were the professor and only had certain time slots available, what would you do and what would you want as a reply?

(Surprisingly, none of the 5 existing answers mentioned this option.)
Just do both! Choose a time (arbitrarily, if it's all the same to you) and state your availability for other options.

Thank you for the list of time slots, I'll take 08:00-08:30. If anything changes on your side, the other options are also fine for me.

This solves the immediate problem of agreeing on a time and also conveys the information that the other options are fine for you as well.

Note that this advice also applies to non-academic contexts.

Definitely better than my answer!

Deserves many more updoots.

But maybe don't arbitrarily choose the 8 a.m. one (though... I'll admit that I'm biased here).

When someone gives you a list of times to pick from, just pick one.
Otherwise, it just takes two-three more emails to be done with it, instead of being able to close the loop with just one email from you.

Even if they do not give you a list of times, pick one to propose.  Never simply say: When would you like to meet?

An exception would be if more than two people are involved, in which cases selecting all possible time slots that work would be appropriate.

@AnonymousPhysicist ... while making it clear that this is a straw man proposal just to get the discussion started.

@MartinBonnersupportsMonica "I'm free all day tomorrow. How's 14:00?"

If they already offered a few options, simply pick one and be done with it.
But if the opposite happens: they ask you what time to set up a meeting (I assume that the event requires scheduling, otherwise they wouldn't ask). In this case, even if "any time is okay", make a short list of time slots for them to choose from and add that your time is flexible.
The important thing is to reply with information that leads to decision. When it comes to some decisions, people seem to prefer constrained problems than wide open ones, because the cognitive load is smaller, and simulating someone's mind and schedule is tiresome.

Also sometimes professors are so busy that any time is going to conflict with something they were planning to do, so having a limited set of options to choose from lets them evaluate which one can be accommodated with the least amount of disruption.

Since this is a question about etiquette, I would like to say that I personally find it annoying when I offer someone some specific times to select and then they reply "any time is good for me". I consider it more polite to do is to pick a definite time among the options they have suggested.
I might be biased because this kind of situation happens to me quite often. I am someone who does not mind meetings (as long as they are productive) but I really dislike the process of going back and forth to schedule meetings. Giving a list of times is the most efficient way to get that done with. If I take the time to look at my schedule and then identify possible times that will be suitable for me, if the person replies with another email that requires yet another reply, I find that rather annoying.
So, you might have two possible kinds of persons whom you might be dealing with:

If it is someone like me who wants the minimum back-and-forth possible, then a reply without choosing a time is annoying. Even if the person chooses my least preferred time among all the options I gave, I am not annoyed because, by definition, I only offered times that I am willing to accept. If I had a strong preference, I would have said so in my email.

If it is someone who doesn't mind back-and-forth and you reply with a selected time, they will not be annoyed even if you happen to choose their least preferred time, again because it is one of the acceptable choices they offered you.

So, since you are not sure whether you are dealing with a professor who is annoyed by unnecessary back-and-forth scheduling emails or a professor who does not care, the safest thing to do is to just pick a time. That way, you do not risk annoying anyone. And I think that is the intention of your question.

I would like to say that I personally wouldn't want to be a recipient of your offers to meet, because the one who offers a list of times may actually have some minor preferences but is trying to be helpful to the second party, so how can you think a response of "any time is good for me" is impolite, since it gives the first party a chance to pick any time?

@user21820 I have edited my answer to explain in detail why I feel it is impolite to send yet another email when clear choices have already been offered.

Thanks for the edit. It is better but still wrong in its blanket assertion that it is impolite to not pick one of the offered choices. The world will be a much uglier place if we all use your kind of judgement to evaluate politeness.

If any time is good then, imo, the polite option is to say so and pick one anyway.

@user21820 Your concern is well note. I have tried to somewhat soften my language to say "I consider it more polite…" rather than implying absolutely that to do otherwise would be impolite (which is not quite what I said, but I do see how my wording could be construed in that way).

Thanks for your edits, and I am very happy with your current version. If you wish to delete our comments, since they are no longer applicable, just let me know!

Yes, you should pick a time.
The goal of the interaction is to find a fitting time slot as fast and friction-free as possible.
Saying "I am available any time" doesn't contribute much to that goal.
There are two basic scenarios:
Professor gives you a preselection of times to choose from
Here the Professor already gave you all information from their side. If they offer you multiple times, they probably don't care which time you choose, they only selected times that work for them.
If you now bounce that back to them with "I don't care either", you basically didn't contribute to choosing a slot, the Professor now has to choose the slot, and you then still have to confirm it.
Also, a lot of people don't like to make choices that don't matter to them. So just pick a time and be done with it.
Professor asks you to provide a time that works for you
If you respond here with "I am available anytime", that's even worse, because it's not true. I guess, if he picks 3am you won't be able to do that easily, and you probably also have other courses or something else, where you aren't available.
So now the professor has to chose a time that works for them, and then you'll possibly have to reject that date, because you aren't actually available.
So also here, just do as asked, and provide a list.
In general, people prefer you to do as they asked. If they say "Choose a time", then choose a time. If the time slot doesn't work for them, they will either not offer it to you, or tell you.

I don't see any issue. If you are uncomfortable with the phrasing, maybe ask what time is best for them and just agree.
But a time when you won't be interrupted is best, so work time seems a poor choice.