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Scope for the role of peer reviewer
As a young scholar I frequently struggle with knowing the extent to which I should be critical of particular components of papers I am reviewing. I can formulate a rough hierarchy between major concerns (things that need to be changed or this shouldn't be published) and relatively minor concerns (things I think would improve the manuscript, but aren't substantive enough to affect whether the paper is publishable or not).The question here concerns the latter, in essence I don't know where the cut-off in reasonableness should be for minor concerns.
For one example, being curmudgeonly I would say bad graphics are the norm rather than the exception in my field, although they aren't frequently so bad I can't figure out what the author is trying to say. Are minor critques of graphs appropriate (e.g. your gridlines are very obtrusive, the aspect ratio of your chart isn't appropriate, your colors/patterns are hard to distinguish, you should use a dot plot instead of a stacked bar graph, etc.) Frequently my suggested improvements would be somewhat arbitrary though, so I frequently hesitate to give such advice.
Is there any advice to guide the role of the peer-reviewer? Another side question too, does the scope change if I'm doing this for a colleague versus as an anonymous reviewer for a journal?

Agreed - and both questions have good answers. Mods, do you have some clever tool to merge the answers into a single definitive question?

I think everything you're asking about is within the scope of the reviewer's role. Generally speaking, I divide my review up into three sections:
Summary: A summary and free-form critique. Here I communicate what I think the "gist" of the paper is about, its strengths, and offer some weaknesses that might exist in the paper as a whole. For example, if I think the authors were slightly too timid in not offering a interpretation of the data, or if they've missed or glossed over some major point.
Major criticisms: These are things that must be fixed in order for me to consider it a publishable paper, and if I have the chance to review the revisions (some journals do this), things I expect to either see changed, or have very good arguments for why they're not. Stuff in this category includes:

Flawed or inappropriate methods
Major intuitive leaps that aren't supported by the data or analysis
Study design problems that need attention
Major failings of interpretation
Journal specific problems, like failing to properly report your protocol to established standards for a clinical trial, or the inappropriate use of p-values in some journals.

Minor criticisms: These are all things that are essentially "The advice of someone reading your draft with a critical eye". Importantly, these are things where, if they all made it in, while I would possibly be annoyed, I wouldn't be upset that the paper hit the press. This does include things like advice on graphics (my pet peeve is graphics that are unintelligible when printed), missing citations, etc. Things that are above the level of a copy editor, but aren't going to move my decision on the paper one way or another, unless there are a lot of them.
Occasionally I'll put in one or two small copy editing notes if something jumps out at me (insure vs. assure vs. ensure, etc.)
The cut-off I use is "Will this irk me when I see it in print, and will I think less of the authors that produced it?" To use your example of bad graphs, yes, this would annoy me, and it results in a less usable finding than one with the appropriate graphs - just like garbled language in the Results section might. If its minor stuff, like a turn of phrase I wouldn't have used, or a slight fondness for run-on sentences? That falls below the radar.
As for friends vs. anonymous reviews, I think the scope does change slightly. For a friend, you're helping them polish a paper - I think a great many more things fall under that umbrella, including things like "That's really not what a semi-colon is for" or fiddling with the graphics parameters on a plot. For a reviewer, you're one of the last gatekeepers before this goes out into the world - but you aren't an editor. Your focus should be on the research, and the appropriate presentation of it, unless the errors are so bad as to impede one of those.
In either case, you should be polite.

+1 for "be polite". These are people like yourself, doing their best to publish their work. Treat them with the respect you would accord yourself.

+1 for asking "Will this irk me when I see it in print, and will I think less of the authors that produced it?"

Please see my answer to a similar question on the theoretical computer science SE site.
At @David's suggestion, I'm copy-pasting my answer here, but keep in mind that the question is slightly different, and my answer is aimed at theoretical computer science.  The bold questions are quoted from the original post.  Point 5 is probably the most relevant for this question.
Short version: Be respectful, but brutally honest.

What are the main criteria for determining the significance of a paper's results?  To the best of your knowledge, does the paper make a significant, well-presented, and correct contribution to the state of the art?  If the paper fails any of the three criteria, it's fair to reject it for that reason alone, regardless of the other two.
What are the main elements of a referee report, and which parts are most important?  Here's what I think a report should contain.  Everything should be visible to the author, except possibly for serious accusations of misconduct.
a. A quick summary of the paper, to help the editor judge the quality of the results, and to help convince both the author and the editor that you actually read and understood the paper.  Place the result in its larger context.  Include a history of prior versions, even if the authors include it in the submission.  Be respectful, but brutally honest.
b. A discussion of the strengths and weaknesses of the paper, in terms of correctness, novelty, clarity, importance, generality, potential impact, elegance, technical depth, robustness, etc.  If you suspect unethical behavior (plagiarism, parallel submission, cooked data), describe your suspicions.  Be respectful, but brutally honest.
c. A recommendation to the editor for further action — accept, accept with minor revision, ask for a second round of reviewing, or reject outright.  Keep in mind that you are making a recommendation, not a decision; if you can't make up your mind, just say so.  Be respectful, but brutally honest.
d. More detailed feedback to the author — more detailed justification for your recommendation, requests for clarification in the final version, missing references, bugs in the proofs, simplifications, generalizations, typos, etc.  Be respectful, but brutally honest.
How does assessment for conferences differ from that in journals? Conference reports should be shorter; program committees have hundreds of papers to consider at once.  Whether there should be a difference between conference and journal papers is up to the journal (and indirectly, up to the community).  Most theoretical computer science journals do not insist on a significant difference; it is quite common for the conference and journal versions of a theory paper to be essentially identical.  When in doubt, ask the editor!
What if I don't understand the paper? ...the proof? (Is it my fault or theirs?) If you still don't understand the paper after making a good-faith effort, it's the author's fault, or possibly the editor's, but certainly not yours.  The author's primary responsibility is to effectively communicate their result to their audience, and a good editor will send you a paper to referee only if they think you're a good representative of the paper's intended audience.  But you do have to make a good-faith effort; do not expect to immediately understand everything (anything?) immediately on your first reading.
What about typographical/grammatical mistakes? If there are a lot of errors, don't even read the paper; just recommend rejection on the grounds that the paper is not professionally written.  Otherwise, if you really want to be thorough, include a representative list of grammar, spelling, and punctuation mistakes, but don't knock yourself out finding every last bug.  Be respectful, but brutally honest.
How much time should I spend on a report?  Expect to spend about an hour per page, mostly on internalizing the paper's results and techniques.  Be pleasantly surprised when it doesn't actually take that long.  (If it takes significantly less time than that, either the paper is either exceedingly elegant and well-written, you know the area extremely well, or the paper is technically shallow.  Don't confuse these three possibilities.)
How many reports a year am I expected to write?  You should write at least as many referee reports as other people write for you.  If this takes more time than writing your own papers, you're not spending enough time on your own papers.

links with no explanation are generally not preferred; why not just copy-paste?

PLoS Computational Biology editor P.E. Bourne has written a series of very decent “Ten simples rules to …” articles. There is no detailed guide to being a good reviewer, but Ten Simple Rules for Reviewers sure is a good starting point. Summing it up:

Do Not Accept a Review Assignment unless You Can Accomplish the Task in the Requested Timeframe—Learn to Say No
Avoid Conflict of Interest
Write Reviews You Would Be Satisfied with as an Author
As a Reviewer You Are Part of the Authoring Process
Be Sure to Enjoy and to Learn from the Reviewing Process
Develop a Method of Reviewing That Works for You
Spend Your Precious Time on Papers Worthy of a Good Review
Maintain the Anonymity of the Review Process if the Journal Requires It
Write Clearly, Succinctly, and in a Neutral Tone, but Be Decisive
Make Use of the “Comments to Editors”

I would add: carefully read both the “instructions for authors” and “instructions for reviewers” of the journal you are reviewing for, if you are not already very familiar with them.

There are certain things I look for when reviewing papers that are "show stoppers", i.e. if I find one of these, I usually recommend rejection.

Things that don't add up, e.g. fractions that don't add up to 1, unreasonable large performance improvements such as orders of magnitude when the proposed method would save 50% of the work in the best case.
Major omissions, i.e. something that would be required to reproduce the results/implement the method is not described adequately.
Wrong or unjustified statements.

The things that don't fall into this category (e.g. graphs that are hard to read) are usually not a reason for me to recommend rejection, unless they occur several times throughout the paper. The same goes for bad spelling/grammar.
I would always point out things like you mention as example (one particular thing I don't like is graphs with different scales next to each other to compare two approaches) if you think that changing them would make the paper better. In the end, everything is subjective and may seem arbitrary.
I would use the same diligence regardless of whether looking something over for a colleague or reviewing for conference/journal because even in the former case the paper will presumably be submitted somewhere where it will be peer-reviewed.
In summary, I think that there need to be a number of minor concerns throughout the paper to recommend its rejection. One or two graphs that look odd would for me not be a reason to do so, unless of course there are other, more serious problems.

Here is the rough checklist I use for refereeing. I work in mathematics, so it may need adjustment for other areas. When I write a review, I imagine it is for my own paper, and I try to include the things that I would like a reviewer to include for me.

Is the paper correct? Trivial errors can be corrected in a resubmission, of course. I have not yet received a paper in which I found any serious error.

Part of correctness is clarity. I consider the average readership of the journal (to the extent I can), and any aspects of the paper that would be unclear to them can be raised in the report. There is a difference, of course, between unclarity and writing style. But papers should use standard terminology when it exists, and proofs should be written in a way that is not unduly difficult to follow. Occasionally, a referee can suggest a more streamlined proof, which is fine.
I keep a running list of typos, style errors, and other trivialities, which I list at the bottom of the report with minimal commentary.
I do not check the correctness of all bibliographic data, but I often refer to one or more of the references when reading the paper. If I notice any errors in the bibliography I note them in the report.

Is the paper complete?

Are there any obvious gaps in the research? For example, if a theorem has a strange additional hypothesis, the author should address the necessity of this hypothesis, or consider stating it as a question. Nobody else will be able to publish a paper to fill in minor gaps, so it is important for the author to be sufficiently thorough in the original paper, for the sake of the overall literature.
Are there additional references that should be cited? If I know of additional research that the author has not mentioned, I can raise it in the report. I believe this is one of the more important roles of the reviewer, because no author is aware of the entire research literature.

Does the paper fit the journal to which it has been submitted?  I have a general feeling for the differences between the journals in my area. Most journals have a statement of scope and purpose on their website, as well. For some journals, I think that all professional-quality, on-topic papers are in the scope of the journal. But for "high-tier" journals, the paper needs to have sufficient results (and, perhaps, a sufficient density of results) to fit.

The degree of completeness (item 2) can be important here.  The editor will make the final decision, of course, but it is not inappropriate for the reviewer to indicate if they think the paper is correct but not a good fit for the journal to which it is submitted.
If it is clear that a paper is not a good fit, I may write a report indicating this without verifying the correctness of the results. This allows the author to resubmit to another journal more quickly than if I took my time with the paper.

Did the editor give any additional instructions?  For example, one top-tier journal explicitly asked reviewers to raise the quality level required for acceptance, because the journal had a long backlog and wanted to reduce the volume of accepted papers. Other uncommon situations can arise, which the editor may summarize for the reviewer.

I attempt to answer questions 1 and 3 in the first paragraph of the review. These are what the editor needs to know. The lower parts of the review are intended more for the author, and may have remarks related to possible changes or additions, particularly if my recommendation is to revise and resubmit.

+1, though I don't think assessing the paper's fitness for a certain journal is the task of a reviewer. If a paper isn't a good fit, it should lead to a desk reject by the editor, without involving reviewers. When you really question the fitness of a paper for the journal at hand as a reviewer, I think it is more appropriate to contact the editor about the matter first instead of proposing a reject straight away. It is possible that your view of what should be in the journal is skewed. It would be a shame if authors get punished for that.

If you decide that a particular paper you're reviewing is acceptable, then your job as a referee of the paper becomes to suggest improvements that you think will substantively help the presentation of the scientific content. Even minor corrections like the ones you've listed can be considered substantive when they lead to "real" improvement.
For example, I'd argue that suggesting a comment that axes labels should be 12 pt instead of 7 pt would be appropriate, as it would substantially improve legibility; however, arguing for 12 pt instead of 13 pt is not significant enough to make a real difference. Similarly, I would point out grammatical or spelling mistakes if they are relatively few in number, but make a general comment if there are many, because I'm not being paid to be a copy editor. (As another example, Oxford commas wouldn't rise to that level, unless it's an "Eats, shoots, and leaves" issue.)
In general, however, there isn't anything that is really too nitpicking in nature unless all you're doing is expressing a personal preference.

If these are suggestions rather than mandates (as you suggest) and if you are willing to commit the time to providing such feedback, I'd say go for it. It could only help, as long as you're not so picky that the authors end up with a list that is too overwhelming to deal with (not sure where the bar is for that).
FYI: I'm a "young" scholar, too, not a journal editor.

I can also add some other pointer I've come to learn over the years on what constitutes a good reviews.
Things you should avoid:

Rejecting the paper because you did not like the approach (science is not about liking, is about correctness)
Rejecting the paper because it has many typos (you can always ask for a spell checking, but if the idea is good, not being a native speaker shouldn't affect you)
Criticizing a paper for not having simple definitions, my rule of thumb is that if a concept pops in a Google search as a wikipedia page, the author does not have to explain it again.

Things that can help the paper:

If the Grammar is poor, recommend some book for writing styles, like Strunk and White, and give some examples on how the paper can be improved.
If you think the paper has some obscure concepts (that did not come up in Wikipedia) ask for clarification.
The paper, as a rule, should be implementable by someone who has the expertise in the area.

My main criterion for such concerns over clarity and presentation is
reader time: is the time it takes the authors to address your concern comparable to the (cumulative) time gained by the paper's readers.
This also means: the larger the expected audience, the more you can nitpick.

What is the "time gained by the paper's readers" and how in the world would I estimate that?


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How do I effectively use tags to organize my bibliography?
I use the online tool citeulike to manage my bibliography. The main tool to organize the library is tags (functionally equivalent to tags here on this site). One problem I seem to be having is I do a very poor job of initially choosing tags, so I need to continually re-tag my library to keep it organized.
Is there any advice on choosing an intitial set of tags? Or will it be necessary for me to continually maintain my library to keep it organized/updated as much as I would like?

I am not sure what answer would satisfy you. People have different conventions when it comes to tagging. What is your particular problem with your current tagging scheme? (And why do you need to retag things?)

@PiotrMigdal, I am aiming for advice about prospectively identifying tags or tag-systems that would be useful (beyond say key-words for articles). I need to re-tag things because I don't always know ahead of time what specific content of articles I would like tagged. For instance, I might say tomorrow I want to identify all of the articles in my library that have used cross-sectional analysis (versus longitudinal) for a specific project I have in mind. I did not make such tags initially, so I need to go back and re-tag if I want this information in the future.

I'm not sure what answer would satisfy me either. I figured this would be a good community to ask if anyone has developed any more formal system (I certainly haven't given that much thought to it). Although I doubt a perfect example exists that would fit my need, any advice about "tagging conventions" and why they are useful for any particular case I suspect would be insightful.

How about using multiple tags, some very general (e.g. sequence analysis) and some exactly related to your projects (with their names)? Then, after some time, you can search either for its general content (it was about X) or by your former project (I used it for Y). Does it seems OK? (I like tags and tagging but I cannot say much besides that redundancy is often usefull; e.g. for my delicious account I use typically 5 tags per webpage).

@PiotrMigdal, that seems similar to what I am doing now, it doesn't help with the prospective tagging part though (in essence I don't do a good job of foreseeing future projects). It may be that I should expect to have to go back and re-tag (hence I should spend effort making a system that I can re-tag articles in a fairly trivial way).

Well, no-one should expect to tag with respect to further projects. But when starting a new project you can: 1) remember that you can reuse some stuff (actually it is a followup of the project Z), 2) whenever you  interact with a particular paper (but only then), add a tag describing you new project.

I'd use article keywords with a few meta tags of my own, and call it a day. Consider a desktop based reference manager like JabRef or Mendeley, preferably with in-document search.

@mindcorrosive, perhaps you should formulate that sentiment into a more thorough answer. Why would the capabilities of in-document search make the point of tagging articles moot? The example I addressed to Piotr earlier in my comments wouldn't be resolved with in-document search.

Tagging is only useful if you use it with discipline. Look at Wikipedia or Stackexchange, most articles can be determined by 5-6 categories (science - math - geometry - euclidean geometry - metric). Stackexchange has a max. of 5 tags, often you only see 1-2 on questions, which is often pointless, as those tags will appear often in the question/paper title and abstract too. Wasted time.
So, if you decide to create a tagging system, use at least 4-6 tags depending on how interdisciplinary and specialized your paper/link collection is.
Also consider to not only tag by topic but also kind (review, letter, peer-reviewed, experimental results, theoretical analysis, explanation of new measurement method, meta-discussion...), year, personal rating (very interesting article you learned a lot from and should read again from time to time), rarely/often/top cited, new theory/model, strongly discussed in the research community
A last note. I use myself Copernic Desktop Search as a supplementary tool, I download all papers of possible interest (disk space is cheap ;) ), papers I read, will read or maybe will never take a look at. The point is that Desktop Search software often has more powerful search operators and sorting mechanisms than Google Scholar & Co. If you know how to use them, you can save a lot reading and tagging time or tagging at all. You know, if you are smart in using Google & search operators and have a good vocabulary, you don't have to ask a lot questions on internet boards.
Conclusion:
Don't use tagging for creating a pure thematic and linear directory structure, if finding again your papers or bits of information can be done by learning a good Desktop Search software. Use your tags in a personal way and remember, the point is not to structure your bibliography like a folder directory for categorized files, the point is to find again the bits of knowledge and most memorable papers, which will rather look like a strongly interconnected nonlinear tag cloud. If you look how people tag sites on del.ic.ious, often only 2 or 3 tags, sometimes using up to 10 pure thematic redundant tags, they are doing it imho wrong and waste a lot of time.

Given all of the suggestions to utilize text searches more effectively I might have to expand my tool-box. Thank you for the insight.

The best solution of my is Papers from mekentosj. I should also mention that using tags is not an efficient solution for me; at the tagging moment I could not think about relevant tags and later I would not be able to find the paper. In my system I organized papers in collections (like folders) and search for them using keywords (like one would on in Web of Science) or authors or any other usual field.

I don't see how this answers my question at all, care to elaborate?

You can organize your papers into folders, collections, etc. Then you can search for them using tags you add to the notes of each paper

The same fundamental problem exists whether I use tags or folders (I could create tags to function equivalently to that of folders). I would need to know what folders/collections to create to begin with.

Working with Papers2 I do not care about tags since I do not specify or create any. I create folders for the sake of some organization, and later, when I try to find something, I go to the "search" box and type relevant keywords related with the things I am trying to find. It works usually, at least for me.

So are you saying that searching through documents is a much better solution than relying on tags? I think that is reasonable (one of the comments to my original question made the same suggestion). You should edit your answer to include that sentiment.

I did it, hope it helps

One of the great things about CiteULike is that you can see what papers you have in common with other people, and what they're tagging them as. That can give you a good clue when you're starting tagging.
However, whatever you choose, it will evolve as you aggregate a larger and larger library of references, so don't be afraid to keep it flexible.
In the end, your tagging system will be unique to you, because your interests are unique. For example, in my library, I've got a medical-epidemiology tag, because that covers around 1% of my library. If I had no such papers, it would be a useless tag. If I were doing medical epidemiology research, it would also be a useless tag, because I'd have to apply it to 90+% of my library.
Learn by your own experience: how do you use tags? Which tags have helped you find things? Which tags have you used to try to find things, that turned out to be dead ends?

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PhD duration in the USA
I am trying to find out what the average duration of PhD studies are in the USA. Here in Spain it used to be 4 years, but it seems that Europe is moving towards a 3-year scheme since students are expected to do their MSc before they start. What is it like in the USA? Is some kind of shortening also occurring?

In my university, 4 or 5 in Economics, 5 or 6 in Finance.

Go to scholar.google.com, search "time to doctorate," read papers. Filter by year published to get up-to-date results.

Keep in mind that, in many fields, the time to PhD in the US also includes the coursework (master's) component, so the research phase can be anywhere from one semester to almost two years shorter than the "time to PhD."

The dean of social sciences at my school is an archaeologist and mentioned offhand that his students typically take 9+ years to finish due to fieldwork.

"it seems that Europe is moving towards a 3-year scheme" - I am not sure this applies so generally. In Germany, there is a certain movement towards structured doctoral programs, but newly introduced programs are quite sometimes designed to take four years. Moreover, the practical way these are sometimes conducted is that the doctoral candidate goes through the structured doctoral program for four years, and then remains with his or her department for another year or so, funded from other sources, to complete their doctoral thesis, thus maintaining the original duration of roughly five year

The answer depends strongly on the field, the supervisor, and the dynamics of the research group. You should check the supervisor's graduate students who have completed the PhD. This can be easily done using google or by looking at the web page of the research center in the university.

Each program is going to be different.  Usually, the first couple years of a PhD program involves taking graduate level classes while the later years are dedicated to academic engagement in the discipline (for example, in Chemistry, you would do research in a lab.)  If you have a Masters degree relevant to the PhD, you may cut off some or all of the classroom portion of the PhD program.
The qualifications for actually receiving the PhD also differ.  You may need to get approval from an academic board (this is usually at least part of the process in any case), you may need to write a thesis, you may even be required to be published in an academic journal.  (In the hard sciences, this is common.)
Because the requirements for getting the degree differ, the time may as well.  For the most part, PhDs (with no Masters) should take between 4 - 6 years.  Getting a Masters degree first may cut off about a year or so of that.  While this is generally true, you will find many examples of people taking longer and I've known at least two people who graduated in less than 4 years with a PhD.
While this is an average, you'll want to get info specific to your desired University, the degree, and even the group (or academic adviser) that you choose to work for.

It also varies by discipline.  Some take substantially longer than others.

For US PhD recipients in 2018, the median years between starting graduate school and earning a doctorate was 7.3.  Do not rely on the 4-6 years.

This varies so widely by discipline that asking for an average across all disciplines is unlikely to be very helpful.  Most individual disciplines do keep careful records of this statistic, and it should be easy to search for them on (e.g.) google.
However, I would say with some confidence that no American PhD program requires or even expects its students to complete a PhD in less than four years.  In some programs the "party line" is that it is desirable to complete the degree in four years, but in my experience this means that you start to feel the squeeze of increased teaching and/or decreased funding after four years, not that you get ejected from the program or forced to graduate.
I work in a discipline, mathematics, with a high entry cost but for which, once you acquire the necessary background and skills (with which a small minority of students do enter the program), there is no specific reason why you couldn't do all the work for a great thesis and write it up in a rather short amount of time, say on the order of a semester.  Nevertheless I have met very few people who have completed a math PhD in fewer than four years.  When we get to the upper echelons of talent, preparation and work ethic, this surely must mean that the culture of a PhD program strongly encourages students to stay for this amount of time.
To answer your final question: yes, many programs are trying to shorten their average time to degree as funding is being cut.  In my own PhD program (mathematics at UGA) I was involved in an initiative to do just this: up until recently we guaranteed six years of funding to incoming PhD students without master's degrees and five for students with an incoming master's.  We now guarantee five years to all students.  Note that this does not mean that we do not have funded sixth year students: we certainly do.  But it means that students will, throughout their time in the program, have to keep their eye on the five-year mark, which is something that our former arrangement was not doing: even very strong students would often stick around for six years for no especially good reason.
Finally let me also note that we changed (with my involvement) all our requirements to be independent of whether students arrive with master's degrees.  We have found that the difference in the level of preparedness of such students is not significant enough to justify more stringent time-to-degree requirements.

Many thanks. I find it amazing that you fund people equally regardless of whether they have a masters's; it's very generous. Very informative answer.

I would +1 except for the 4-year hard minimum.  I know several people who did the PhD in three, in STEM fields.  If you're not looking for an academic job afterward, and you know what you want to research, 3 years is realistic in many fields.

@David: There are people who got their PhDs at 20 years old; one presumes they spent a short amount of time in the program.  When I say four years is a "hard minimum", I mean I know of no program in the US which requires or even expects (e.g. by decreasing funding) its students to complete a PhD in fewer than four years.  Do you?

@CesarGon: In mathematics most students don't get a master's on the way to a PhD.

@PeteL.Clark I don't know of any such program.  But expectations and hard minimums are very different, in my mind.  Anyway, <4 is certainly unusual.

@David: My usage of "hard minimum" was not what you were thinking it was.  But this means that the phrasing was not ideal, so I changed it.  (By the way: surely in mathematics we say minima, right?)

This answer is pretty misleading because it refers to four, five, and six years, but for US PhD recipients in 2018, the median years between starting graduate school and earning a doctorate was 7.3.

The Survey of Earned Doctorates (http://www.norc.org/Research/Projects/Pages/survey-of-earned-doctorates-(sed).aspx) has detailed statistics. A summary report is http://www.nsf.gov/statistics/infbrief/nsf06312/ with breakdown by field, year etc.

We generally prefer to have more than just a bare link in answers, since the answer then becomes useless when the link decays.  Can you please add a brief summary of key information at the end of the link?

Thank you. Would you be so kind to add a summary of what the report says, as suggested by @jakebeal?

For US PhD recipients in 2018, the median years between starting graduate school and earning a doctorate was 7.3.

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Is it rude to forward an email message to the original recipient if they did not respond?
If an email message sent to one's professor is not answered promptly, is it rude to forward it without comment to the original recipient as a reminder?  If so, how long should one wait before doing so?  Assume the professor is teaching a class the sender is taking.

It depends on your relationship with the person you're writing to.  But why don't you just include a few lines explaining that you're re-sending as a reminder, or making sure he got the original mail?  It only takes a minute and it's clearly more polite.  I would certainly think higher of someone who does that than someone who just re-sends.

I just checked your profile.  If you are the recipient (not the sender) or such mails, it would be good to mention it in the question.

This question appears to be off-topic because it is about workplace etiquette. The fact that this takes place between a student and a professor is rather unimportant. The exact same question could come up between an employee and a manager. This is far more on-topic at Workplace.SE.

@Szabolcs, yes, I'm the recipient.  I find it annoying but don't know if it's just me.

@StephanKolassa I disagree: the expectations for interaction with students are in many cases very different than in the workplace, because a professor's relationship to a student is very different than a manager to an employee.

On the whole, I'd say "yes, this is a rude way to send a reminder to a non-peer."
The premises are tricky: what is "prompt" to one person is not to another, and not everyone checks (work-related) email at every available opportunity. E.g., some seem to only go through email once a day, on weekdays, or even less often.
There is the other issue about acknowledgement of receipt, even if one's response will be delayed.
But/and if one is teaching a course with 30 or 100 or 250 students, individual responses to daily can be a time-consuming occupation... so that "acknowledgement of receipt" becomes unappealing and an arguable waste of time... if a proper understanding can be reached.
I've tried to cultivate in my students a sense that emails should have a "greeting", a "body", and a "closing", much as old-timey paper letters did... if only so that one can tell whether a thing was mis-sent and/or truncated, not to mention some overt acknowledgement of the identity and dignity of the recipient.
So, if I were to receive a fowarded copy of an email that had already been sent to me, I would consider it quite rude, yes. I do attempt to respond within a few hours of receipt of all email, even if only to acknowledge receipt. Whether or not I had done so, I'd view a merely-forwarded email as uncivil, apart from issues about peer-or-not.

From the point of view of the professor, it would be good to give the benefit of the doubt for the student.   Some students may not be native English speakers, may have a lot of difficulty figuring out the correct and polite sounding additional words when re-sending the email.  They might agonize over it for a while then in a moment of weakness just re-send the email without comment, for fear that their comment might be perceived as less polite than not saying anything.  While by no means the right thing to do, it's not nearly as bad as intentional negligence. I have seen this before.

Perhaps they would think that if the first email wasn't received, or got lost, then the re-sent one might appear as the original and only copy anyway.  Of course in these cases the second email wouldn't be forwarded with Fwd in the subject line and headers included.  Since the OP is a professor herself, it would have been better if she indicates whether the question is meant to be read as "should I be annoyed if I get such an email?".

@Szabolcs: I advise my own students, when they are wondering whether some other faculty person has received an email or not, to resend BUT with some quasi-apologetic words, such as "I'm worried that my earlier email fell into your spam folder, so I'm re-sending it. Sorry if there is duplication..." Whether or not a person is a native X-language speaker, one ought to be aware of the simple niceties of communication and acknowledgement of the existence of "the other". True, many people near age 20 or so "don't get it", but that might be what's being addressed here.

I completely agree with you, I would give the same advice to students.  What I'm trying to say is that if a student does this, it does not necessarily mean that they are being rude.  It might mean that they tried and failed.  I'm hoping most professors wouldn't get angry over this and wouldn't punish the student for it in some way.  I wanted to point this out because it seemed that the OP wasn't asking whether one as a student should do this.  She may have been asking whether a professor should feel offended over it.  Please don't get offended over this as a professor.

Ah, indeed, even if I observe rudeness on the part of a student, I certainly don't react childishly! :) In fact, on many occasions I've "given advice" to people who've sent me clumsy emails, about how to make a better impression, etc.

I would be at a minimum annoyed and further less receptive in such a situation where someone would send a plain forward of an already sent email.
On the other hand, when I need to take such action, I do not send a plain forward but instead I assume the recipient took knowledge of the original email, and add some recent relevant developments (eg: since our last exchange, two new students joined our team efforts and work is really being done. Regarding the original email, everything still stand, please give us an update whenever you can...) or something to that effect


text:
Is it acceptable to email the authors of a paper for the slides they used while presenting it in the conference?
I've noticed that while there's no alternative to going through the actual paper in detail, it often helps if I've gone through the presentation based on the paper, which the authors had used while publishing their papers. (Mostly because, the few presentations on TCS papers that I've seen have good geometric examples/illustrations which may have been instrumental in getting the intuition in the first place, but the brevity required by CS conferences mean very few of them make it to the published paper!)
While a few authors graciously maintain the links of such slides on their web-pages, most do not - and I haven't even seen a single CS conference maintaining such documents on their web-page!
So, I've the following questions:

Since I'm ultimately interested in understanding their work (and extending it if possible), is it considered OK to email the authors for the slides (if they still have it)?
If it is, do I have to justify/explain why I want the slides, or would just a polite request do (with minimal explanations on my part to keep the mail short!)?
Would making such a request more than once make the author feel offended, and/or make them think that someone who can't read papers at the highest level without "assistance" isn't exactly someone worth helping out?
If there are 2 authors listed, without any implications about who is the corresponding author, should I mail both of them at the same time (which may lead to both of thinking the other would be responding), or separately (which may lead to duplication of efforts!)?

I'm not sure what to tag this query with - feel free to re-tag/add more tags as you see fit!

I've had requests by email (or in person, after my presentation) for copies of my slides and even the source code of the tools used, etc. Never was I offended. The reason I didn't put the stuff online in the first place is because it's not clear how many people will want access (is it worth always putting online?). Some workshops provide digital copies of presentations as part of their proceedings or web site.

It's never a problem to ask. In particular if you are interested in extending their work, they should be interested in providing you with more information. Perhaps the extension will happen in collaboration with them, but at the very least you're going to cite their paper. In my experience, views on sharing slides vary, but the objections I've heard related to unpublished material; I understand that in your situation, the material is already published.
I would explain why. It's polite to do so. But do keep the mail short. You could write that if they're interested, you can provide more details on your ideas; like that, you don't swamp them with unrequired information, yet you're open from your side in stating your ideas. Such an offer shows that you trust them, and as they need some trust in you if they share their slides, that is probably a good idea.
I don't think they would feel offended.
Depends on the field. If there is no clear first or corresponding author, I would contact either one of them. They would probably either reply or forward the e-mail to the other author.

To 4, if I saw the presentation live, I'd the person that gave the presentation.

I think it is reasonable to make such a request but your success will depend on how it is done. If you clearly express your interest and reason for asking as well as express your understanding if they were to decline, you have made a humble request which should not offend anyone. If you can I think it would be even better to try to talk to the person directly (putting a face on the request). This takes some guts but is clearly worth it if you think you have significant use for the results of the paper. If you get a no, you might be able to ascertain what the reasons of the no might be, there might be personal or copyright reasons.
The answer to this is perhaps given by 1 already. Yes, short but with enough details to give the person the clear reasons why you would benefit from the presentation.
Turning it into a habit is probably not advisable unless the person you ask becomes more of a mentor than just a source for information. I think most people want something back and perhaps admiration might just not be enough.
I would say, yes, contact both with the same mail. Sending two separate requests would probably just be seen as fishy.

So in short, be brief clear and polite in your request and be honest about your reasons for the request. Just remember that the response will vary from person to person so there is no guarantee for success in every case.

Unless there are reasons that a presentation is considered proprietary (the ground rules of the conference, or it occurred in a non-conference setting, such as a presentation at a corporation or program review), it is unlikely to be a problem to email the presenter for a copy of the slides.
A short note with the email indicating where you saw the presentation, and why you're interested in it, is never remiss, as it shows active interest in the researchers work. With respect to how often to ask, I'd wait a few weeks between requests; otherwise, you will be seen as being a bit too "pushy."
With respect to coauthors, usually the first author is the presenter, unless otherwise indicated. It's probably best to contact the first author initially, and then move to additional coauthors if there's no response.

If this is theoretical computer science, then the author order would usually be alphabetical.


text:
What kind of opportunities exist in the industry for someone with a Ph.D in theoretical CS?
I'm curious to know what kind of choices does someone with a recent Ph.D in theoretical CS have, in the industrial research labs, and how to find out about existing opportunities. In particular, I'm looking for:

Links to sites where such opportunities are listed, if something like that exists.
Information regarding the scope of working on pure theoretical topics in industrial labs, which tend to be product-oriented IMHO.

It would be really great if anyone working in an industrial lab would share his experience (which lab, what kind of work you do etc), even if he/she may not be working on theoretical CS (or CS at all!).

+1 This style question is very useful, and should (and will) be asked for numerous fields of research.

I think the title to the question is unintentionally misleading.  What matters is not whether your PhD is in theoretical CS, applied CS, math, physics, etc., but what you know and what you want to work on.  There are hotshot programmers who have degrees in theoretical CS and are happy to work on real-world problems.  I think you're asking: "What PhD-level industry job opportunities are there in theoretical CS?", which is a different (but dandy) question.

@espertus - The title is intentionally worded this way! I wasn't implying at all that I would want to work on "theoretical" problems (i.e. not involving coding/prototyping), but that I'm open to any kind of work in industry that would utilize a theoretical background in CS. Btw, I could go on a bit about how the intersection between "theoretical" problems and "real-world" problems is not a null set, but this is not the place for that !

@shan23, absolutely.  A knowledge of algorithms, graph theory, probability, etc., is vital for solving non-trivial real-world problems.

@shan23 maybe you were the one who asked this question over at cstheory ? http://cstheory.stackexchange.com/questions/5293/is-a-phd-in-tcs-the-best-way-towards-achieving-a-career-in-industrial-research

@Suresh - Yep, as academia.SE didn't exist back then! It is similar to his, but not exactly the same query...

AT&T, Google, IBM, and Microsoft all have thriving basic research labs that regularly hire PhDs in theoretical computer science, and whose members regularly publish in theoretical computer science conferences and journals.  Yes, research at those labs is colored by the needs of their parent companies, but not as much as you might think.  All four companies (and several others) have thriving internship programs.
As with any other research job, your best bet in finding opportunities is to talk personally with people at the labs.  Go to FOCS/STOC/SODA, sit at the same lunch table as David Johnson or Muthu or Ken Clarkson or Yuval Peres, and just talk to them.  (It obviously helps if you have some research results that they care about.)  Ask your advisor to introduce you if you don't feel comfortable just introducing yourself.
(I'm about to get some angry emails from David, Muthu, Ken, and Yuval, aren't I?)

+1 for being specific - that's exactly the kind of answer I was hoping this question would generate!

I work at (but do not speak for) Google.  While Google does hire people with degrees in theoretical CS, you also need to know how to program well in order to get hired.

@espertus - Thanks for affirming it - I'd have anyway ensured my coding skills did not rust while in grad school!

I would strongly suggest you to join ACM (Association of Computing Machinery). The organization focuses on the advancment of Computer Science both as a Science and profession. Join the community and mingle with experts, share your knowledge and skills with them.
You can also find a lot of opportuites on their jobs page as well. Wish you all the best in your career!


text:
How do I teach a course that has an extremely clear textbook?
I have decided to use Head First Android Development for my mobile application development course this spring. Like other Head First books, it is easy to read and understand. In my 15+ years of college teaching, I have never before found myself in the position of not needing to explain the textbook to my students (perhaps because this book is written for a general audience, not an academic one).
In typical classes, I assign reading before lecture (sometimes with questions to force students to at least skim the material) and then spend lecture explaining the harder material from the book, providing illustrative examples and having students work simple problems.
While I could present the examples from the book, I think that would be babying my students, who should be perfectly capable of reading such material themselves. (This is an upper-division capstone course, with many prerequisites.) The subject matter does not lend itself to doing small-scale exercises with pencil and paper, the way I would when teaching computer architecture or programming languages. While I plan to have some guest lecturers, I can't do that every class session.
The class will have about 25 students in a traditional classroom, not a computer lab. Lectures are 75 minutes long, twice a week.
What do other teachers do in this situation, or is having a clear, understandable book unprecedented?

From the point of view of a relatively recent CS student, please don't be a "textbook teacher". I want to learn things that can't be found online or in print - things that aren't just a quick search away. Make your classes exciting and interactive, but not in a socially pressurising way. For example, 'gamifying' your classes could be particularly effective on this topic. Having a clear textbook is by no means a bad thing - it's your job to make the subject approachable and that only serves as evidence of how accessible it really is.

For many classes, one doesn't have the students read the material beforehand.  I personally am having students do that in my classes this semester, but I'm also not typically lecturing.  If you are lecturing, I feel it is often counterproductive to make students read the material you will lecture on in advance (the ones that get the reading won't get much out of your lecture, and some of the ones who don't the reading may be wasting their time).
The main thing I suggest is to think carefully about what are your goals for the class, and use that to guide your course design.  (Are the goals just to have the students understand what is in the book?  Or something more?)
Here are a few concrete possibilities to consider:

Don't make students read the book in advance, just lecture.
Cover some of the material with out-of-class readings and some with lecture, and maybe have students present some of the material.

Or if you really want them to do a lot of out-of-class reading:

Even if it is a normal lecture class, you can treat many of the classes as labs, and give the students mini-projects to do (possibly in groups/pairs).
Since you said non-computer exercises aren't appropriate, come up with meta-exercise questions for students to discuss in groups (what are pros/cons of Method X?  how would you design Y?...)
Spend a little time reviewing the reading and design lectures around additional applications of the material.

Right.  Rather than asking yourself, How do I fill up these 50 minutes, ask yourself what learning and sharing activities would be productive, and then ask yourself if there is any background knowledge you should make sure everybody's on the same page about before doing them.  Will this course provide opportunities for the students to take a more active role than in the traditional college class?

Thank you. I've switched the location from a classroom to a computer lab so I can have students try things out during class.


text:
Do school-wide holidays count against personal vacation time?
I keep hearing different things from different people and it seems there is no clear policy laid out at my institution regarding the definition of graduate student vacation days; I'm curious how PIs and students handle this issue at other places.
At your institution, do University-wide holidays (such as "Spring Break" or "Winter Recess / Christmas holiday") count towards a graduate student's two weeks vacation?  I always thought the expectation was just that you should be working most of the time, regardless of what day it is, and that seems reasonable to me as long as students have flexibility to take leave when they want/need to without somebody nagging them about the specifics of when/how much time off.
However, recently there's been the assertion by certain bean-counting PIs in my department that students should be working 6 days a week (including nights) and only taking 2 weeks of leave in total (including major holidays).  Most people probably work about this much anyway, but being told that it's required leaves a bad taste in my mouth.  If people want to get really specific about the "number" of days worked/not-worked, there should be a more standard definition of what comprises a work day (i.e. 9-5, not 9am-12pm).  Am I way out of line here?

This is not meant to be an official opinion, since obviously the rules depend on the local labor laws.

We should distinguish school holidays—days on which classes are cancelled—from official holidays, on which the university offices are closed.
A graduate student not working on a school holiday would be counted as taking leave; however, when the university is closed, that is not normally expected to be a working day for anyone, and thus students would not use a vacation day in such a case.
Advisors should not have policies in place that expect students to be regularly working six days a week, particularly since that would mean that they are potentially in violation of a whole bunch of labor rules.

Given that information, my personal opinion is that research cannot be done according to a timecard. There will be days when you go into the office and figuratively spin your wheels all day, and there are days where you are firing on all cylinders and getting tons done. In my own group, so long as someone:

is prompt in answering requests,
attends group functions,
lets me know if he or she will be out of the office for extended periods, and
is getting his or her work done,

then I will let that person work in whatever manner is most conducive to getting the job done. That's more important to me than knowing they clocked in 8 hours per workday.

I would answer with a definite No, but check with your graduate student handbook or university's graduate student policy documentation to verify.


text:
How can I encourage my advisor to adopt better work practices?
I'm a second year PhD student.  In general I love my advisor, but recently we've run into some small bumps in the road while working on a paper together.  He's controlling the "master" copy and I send most of my contributions and comments through email for him to incorporate.
A few days into the process, we had a conversation that went something like this...

Me: "Hey, so I cited a few papers you might not have seen.  How do you
  keep track of your references?  I use JabRef to keep up with BibTex
  entries, but I can export those citations to a bunch of different
  formats..."
Advisor: "What are you talking about?"
Me: "Like, when you need to
  make your references section... how do you keep track of all the
  papers you've cited in the text? Refworks? Endnote? Zotero?"
Advisor: "What?  ...I use
  the 'copy/paste' method."

I was baffled by that answer.  I know he's been doing this for a long time with good success, but I cannot fathom someone who has been collaborating with so many people for so many years is still at the level of manually formatting each entry in a Microsoft Word document and then copying/pasting over whenever that reference is needed elsewhere.
Any suggestions on how I can help bring this faculty member into the 21st century without seeming presumptuous?

maybe it's a topic for a new question, but why using endnote etc? Copy/paste from a (paper-specific) bibtex sounds quite simple to use..

Ran G, he isn't using bibtex (I wish!).  He's got a giant Word file of manually formatted bibliography entries that have to be individually copied out and reformatted for each submission.

To ease the transition, try 'Google Docs' - you can always 'format' the paper later

@PhD I don't see how Google Docs is of any relevance to this question. OP is asking how to educate her supervisor to the use of a decent bibliography management tool.

You are presumptuous by thinking that you 'need to bring the faculty member' into the 20th century. Everyone works differently, and as a PhD student its important for you to realise this earlier rather than later and respect/learn to adapt to these differences.

Actually, very few of my colleagues use a bib manager, even recent Ph.D's. I find it unbelievable but this is up to them. I am now refusing to to work with one group as the manuscript management is so poor and wastes months of time and errors never get fixed. For example, I just got a paper after a year and every reference with more than one author is still incorrect. I would say manuscript management in a team tends to default to the least proficient member and I am finally starting to take a stand against this (waster your time but not mine kind of approach).

It'd be a different question if the advisor's response had been "I prefer plaintext over endnote etc.". In this case the advisor seems unaware that other tools exist.

Turn the tables.  For your next paper, you maintain the master copy.  Make sure all the infrastructure is in place, including a fairly solid draft of the paper, before you involve your advisor in the writing process at all.  Use whatever version control and reference system you find most useful.
Your advisor may simply refuse to use your tools; fine, you can still incorporate their emailed inputs.  Or they may just need someone else to figure out the infrastructure and teach them how to use the tools, instead of figuring it out themselves from the manuals.  Either way, you'll have some extra work to bring your inexperienced (and possibly resistant) coauthor up to speed, but that's a standard part of the student-advisor relationship.
In the worst case, your advisor may simply refuse to give up control of the master copy.  (Never mind that it's already too late.)  In that case, you may need to encourage them to look for another student.

+1, except for the last part.  In my opinion, this is not a big enough issue to merit changing advisors.

@DavidKetcheson: That was half-joking, but only half.  An advisor that refuses to let students take control of their work is doing the students an immense disservice.  At least in my own subfield, I would definitely warn students away from such an advisor.

Thanks, JeffE.  I will definitely keep this in mind next go-around.  I think this prof is amenable to change but afraid of the technology (as SteveP suggested.) After posing this question here, I offered to handle the bibliography because I already have most of the references in my system and it would be easy for me to do put it all together quickly.  He seems interested.

I disagree only in that your method may not actually be regarded as 'easier' than what your advisor is doing. You're making assumptions about how someone should work.

@JeffE said this, but just to make it clearer, I would strongly recommend saying "if the tool misbehaves, just send me an email of your changes and I will make them". This provides an extra level of support which means the supervisor isn't going to be stuck in tool hell. This is probably more important for tools like git/hg, where as a beginner I occasionally had to make a local copy, blast my whole repository away, and start from a fresh checkout.

I love automating things. However, automation requires lots of context which you either need to learn or know (if you did it yourself). Not everyone is willing to make this investment for a one-off job or a possibly unsatisfactory experience. I am very selective in what software I become expert in, but when I decide to go for it, I go all the way. I did not wish to be wasting my time in shallow learning of yet another software; although with less time available, I am now beginning to do it, but also because, lately, user interface design has become more accessible for shallow users.

This probably sounds defeatist, but you might just have to accept the fact that some people would rather do things the hard way because they fear that the technology will eat up more time than it's worth. Maybe after building more rapport with him, you will have an opportunity to demonstrate the value of your method...for example, if a paper gets rejected from one journal and you can reformat the references in a few minutes, whereas it would have taken him much longer.

Once I tried to get my team to use Zotero for biblipgraphic citations. It worked except for one instance of one reference. That one instance of failure was enough to convince the advisor to never give it a second chance.

Endnote doesn't work on linux. Refworks came into existence in 2001 and is a website, it could disappear any time. Zotero is only 6 years old.
Programs come and go, websites come and go. Text files keep working. They are easy to search, easy to maintain, easy to move between operating systems.
Your supervisor has been around a lot longer than you. Perhaps they have discovered that fancy databases are not worth the extra work they involve, particularly if (like me), they've had a couple of products they love get discontinued over the years.

Endnote isn't just a website, it is also a downloaded software that can also be incorporated into word. But I agree, systems change/operating systems change, and in this day and age it's quite rapid there's sometimes no point in trying to keep up.

Any suggestions on how I can help bring this faculty member into the 21st century without seeming presumptuous?

You can't. Your attitude is presumptuous.
I, for one, still live in the 20th century. I personally prefer the copy-paste method to BibTeX, despite having used BibTeX for multiple different projects. This is on the grounds that it doesn't give me additional files to juggle, and if I have weird references I can easily put them into the bibliography as I think they should look without having to look up the BibTeX documentation.
I'm happy to use BibTeX in my joint papers whenever my collaborators prefer. Typically, when it was `their turn' to handle the document they separated out the bibliography into a BibTeX file, and then I followed suit by adding to it whenever I had additional references to cite. Sometimes my collaborators stopped to ask my permission, which I've always cheerfully given.
I also used a more sophisticated online collaboration tool once when another one of my collaborators set up our document using it. Once again, I prefer to do things the old-fashioned (i.e. ten years ago) way but I was happy to adapt to my collaborator's preference.
Can you "fathom" my preference? Whether you do or not, I concur with JeffE -- if you want things done your way, ask to be in charge, set things up yourself, and then let your advisor know what you've done. Maybe your advisor will adopt your tools permanently if he/she ends up liking them, maybe not.

Maybe you should get your advisor to use something like svn or cvs with the ability for anyone to edit the "master copy". Then you can slip in your refs as you see fit.

Getting him to use version control is probably going to be harder than getting him to use bibtex.  If you you try, you might as well go for Mercurial or Git while you're at it.

@CharlesMorisset Yes, Mercurial and Git are harder than SVN in the same way that Bibtex is harder than copy/paste.  The up-front investment is more substantial, but the long-term payoff is substantial (all of this is IMHO, of course).

While I  haven't switched from SVN (and this thread is getting dangerously off-topic), one potential advantage of Git is that it encourages micro-commits - these are handy when doing lots of edits.

People who are scared of svn are often not scared of Dropbox, and that provides all of the common editing you need for this basic task.

(even more off-topic) -- if you are going to try moving an academic to git/hg, then say to them "if you get a merge conflict, just send you latest file to me and I'll fix it". If you have made a set of micro-commits, and every single one of the them conflict (for example due to a global line-ending change or reformatting), making all the merges can be very painful.

I'd like to give the opposite answer than JaffE's.
You can't, give up.
unfortunately, the relationship between you and your advisor is not symmetrical. You can try to make him/her change his/her ways, but if s/he is not willing to change (and habits are difficult to change), you'll end up just fighting windmills

[blank stare]  Oy.

Advisors are often just busy. And they'd be quite happy to give up control of it saves time.

I agree with anonymous.
I'm a young academic but I actually prefer the old copy and paste/formatting by hand over a program that will do it automatically. For me, I've found that generally, the copy and paste format helps in catching errors and is easier to use than an embedded software program that has the potential to crash/become buggy.
I've found that with a variety of those bibliographic programs, they are great for data-basing your entries but not very intuitive or easy to use when it comes to actually writing papers in programs like Word or OpenOffice. They don't always do well in crossing other computers depending on the programs various individuals use (i.e. some might have a mac and use OpenOffice, while the other author has windows and uses Microsoft). The compatibility can cause issues, and many academics use different programs (for example, you use BibTex, my university uses Endnote, my undergraduate uni uses Refworks).
I've also found that while programs such as Endnote can 'technically' adopt styles for a specific journal, the output is never 100% to what the journal requires. It's just easier to type it in right the first time for me, than to try and use a finicky program that can actually cause more, rather than less problems.
You should not rely on these programs to provide you the EXACT formatting required for a journal, in many cases you need to go back and fine-tune. For example, I recently submitted a paper to a journal that wanted a particular style, my referencing program was able to 'output' to this style for the journal, but it wasn't exact even though it had the journal listed as a type of output format. I had to go back and manually format each entry to ensure consistency with the latest printed issues. As I was hand-typing my in-text citations in the exact way as the journal wanted, it wasn't much formatting that needed to be done for the end.
I don't have any issues in keeping track since I use a bibliography program for a database, but tend to add the entries in after the journal article is submitted for review. I just keep track using a plain old word doc, and part of my revision strategy is to go through the paper and find every reference and cross match to make sure I haven't missed any. This also allows me another chance to see any language etc issues that might need fixing up.
I think you need to take a step back and consider that not everyone works in the same way and what you might consider as 'easy' could actually be more difficult for someone else who may have a different way of thinking. Some academics use a multitude of programs, some still prefer more traditional methods and some might jump on board with innovation, and this isn't necessarily a generational gap either.


text:
Will people judge me negatively for skipping department seminars?
I'm a graduate student in the Earth Sciences.  The breadth of my departments runs the gamut from geobiology to geophysics and everything in between.  As a result, a large number of the department seminars that get hosted are on topics that I have little or no background in and do not relate to my research field in any way.
The expectation seems to be that everyone should go to these type of events to stay abreast of major events and gain some breadth of knowledge, but whenever I go to one that is far outside my sphere of knowledge I end up resenting the wasted time.  To me, it seems like a huge waste to sit through a 60 minute talk on something I don't have the background knowledge necessary to understand in even a rudimentary way.  Sometimes this is the fault of the presenter for not preparing a talk for a broad enough audience, but with biology talks I know that the fault is my own.  Don't ask me the difference between a protein and an amino acid; I have no idea!
So lately I've felt a strong temptation to blow off some of these events reasoning that it would be vastly better to get in another experiment that day than go sit through a lecture I'm not equipped to understand.  But I'm worried that other people will think I'm being a slacker as a result.
Do you look down on colleagues who sometimes skip out on talks far outside their expertise?
And, Is skipping an event like this better or worse than showing up but discreetly reclaiming time during bad talks by studying on a smartphone?  Obviously, whipping out a laptop during a lecture would be very rude, but flipping through flashcards on my ipod while sitting in the back of the hall would be a low-key way to reclaim some of that time during talks when I have no idea what they are talking about.

There are usually one or two such events per week.

I would say that you should always go to seminar, unless you have some very compelling reason not to go (you are away, you are working on an experiment, you are trying to finish writing your thesis, etc.).
There are four reasons:

Scientific courtesy. To travel somewhere and give a talk to the 10 people who show up (5 of whom you already knew) is really irritating.
Good or bad -- you learn something about presentation. Even if you say "wow, I should never do that in a talk" your hour has been well spent.
You get perspective. You never know when something that someone says will make you see your own work in a different context.
The speaker may someday be interviewing you for a job. It's better to be able to say "I heard your seminar" than "Oh, sorry, I missed your seminar when you visited."

Four is a great reason that I never considered before.

Try to always go.
If you're a first/second year grad student, go because you have to.
If you're a third/fourth year grad student, go to learn about disciplines and topics other than yours.
If you're a fifth+ year grad student, go to network.

Let's ask another question: is there at least one good reason not to go at the seminars?

Time consumption: except if you have a 1 hour seminar each day, you can probably afford the time loss due to the seminar. BTW, it it a time loss only if you go and don't speak to anybody, don't ask questions and don't try to understand a little piece of what is presented.
It is not profitable: really? A lot of research results start with ideas from elsewhere. Of course, it can be different for earth sciences. Even if you don't see something directly useful, you will probably be confronted to different ways of thinking.
"I am going to the seminars with my laptop/smartphone, people will think I am rude": and they will be right if you use your laptop for other things that taking notes about the talk. To be fair, this can be considered OK to go with your laptop for working during the talk if your the dean, or the head of the department...

Well, in fact I cannot see good reasons not to go, except if it takes you 5+ hours a week...

Well, there is no universal advice. In general, you should adopt the local policy. If it is really the expectation, then you should go. Try to ask your younger colleagues.
Of course there is an other aspect: usually you never know in advance whether the talk will be good and inspiring or not. Usually it is not, but sometimes there is a surprise. Most of us go to these seminars hoping for a miracle. Unfortunately, in most cases the talks are simply bad.
Finally, there is also the argument that later you will be also giving talks on similar seminars. It is somehow sad if nobody except your fellow buddy listens to your talk.

Ask older (more senior) colleagues?

Part of being a grad student is politics. Skipping out on seminars signals to the presenter that you are not interested (which is probably true). Depending on the personality of the person, it may make them an enemy. In academic politics, revenge is a dish served cold.

Is skipping an event like this better or worse than showing up but discreetly reclaiming time during bad talks by studying on a smartphone?

If the presenter is an older person, screwing around with your cell phone will be perceived as terribly disrespectful, and much worse than not showing up at all.

But I'm worried that other people will think I'm being a slacker as a result.

The perception will come across more as "he is not one of us". That sort of attitude is the kiss of death when it comes to recommendations.
My advice is to suck it up and go to them. It is part of the cost of being a grad student.

Opinions on others may depend on many factors. Some people may not care at all (or even does not notice), but generally not attending seminars may be viewed as

lack of commitment,
lack of genuine interest in research by other people and in other fields,
general laziness,
lack of respect for work by other people,
you not feeling being a part of the department.

And while you may care less about the opinion of your colleagues, the opinion of your advisor may matter a lot.
If everyone knows that a certain seminar is of very poor quality, perhaps the reaction may be not so severe. However, I guess here it is not the case:

Don't ask me the difference between a protein and an amino acid; I have no idea!

It is a sign that even more that you should the seminar. Not knowing sth simple - check wikipedia or ask your friends. Not knowing something more advanced - ask the lecturer (as (s)he is there exactly to explain you, among the others, a certain topic).
Comment:
for some reason other answers do not cover the question, which was spelled out three times:

Will people judge me negatively for skipping department seminars?
Do you look down on colleagues who sometimes skip out on talks far outside their expertise?
Is skipping an event like this better or worse than showing up but discreetly reclaiming time during bad talks by studying on a smartphone?

Concerning your last comment, I thought that my answer was clear that I think that yes, they will judge such behaviour badly. For what it's worth, I made presence to seminars mandatory for my PhD students, and highly recommended for the postdocs.


text:
What is the purpose of the weekly research meetings that advisers often have with their research group?
Does it usually happen even if all of the adviser's students have very different research interests?

These meetings can serve a variety of purposes, but many of them fall into the broad category of keeping the adviser and all the group members updated on what everyone in the group is doing.  Below are some of the secondary benefits of a group meeting:

saves the adviser time (compared to meeting with students individually)
motivates the students to keep doing work, so they have something to report at the meeting
fosters a sense of community with the group
provides the students experience giving informal presentations
often leads to the more senior students mentoring the junior students

To answer your follow-up question in the description, no, some faculty meet with each student individually; in fact these separate meetings are common, for example, in mathematics.

Also, meeting as a group (or more generally building a community within the group) often leads to more collaboration among the group members, which in turn yields more and better results.  Also, sunshine makes the best disinfectant.

"saves the adviser time" or, in the case of a former boss--who shall remain nameless to protect the guilt--it allows the adviser to waste as much of everybody else's time in one go as possible. I am actually a fan of these meeting, but some people just don't have what it takes to run them well.

One trick I've used is to allot 5 minutes to each person. So (a) meetings don't go on forever (b) you have to distill things down to the essence. (c) you have to assume that context exists.  I have individual in depth meetings with students as needed

In a research group with widely varying research interest, I think the "sense of community" and "mentorship" are probably the most important outcomes of such research meetings.

As one of these advisors who has both individual meetings with students as well as group meetings, I can attest that I use the group meetings more for skills development rather than just rehashing research-related issues.
It serves a number of purposes:

Presentation of skills and tools that will be useful to the entire group (for example, in my group, that means programming tools, content management software like Git or Subversion), as well as things like "How do you write an abstract?"
Presentation by group members of their own research work
Presentation by group members of other people's work (often through a discussion of a paper in the literature, or a group of papers clustered around a common topic)

Now, my group happens to be bifurcated in purpose: I have people working in two very different application fields. I still have everybody present to the entire group for the simple reason that if they can't inform group members with whom they have methods and techniques in common about their research, how are they going to explain their work to anybody else?

Aside from Dan's answer, which is probably one of the main points, having the lab members present in group meetings also helps significantly in developing public speaking skills in a low-pressure environment. Many of the lab meetings that I've attended focused on the ability of the presenter, often a graduate student, to present an idea clearly, concisely, and persuasively. As an added bonus, at well-run meetings, there are often many questions, which helps the presenter learn to field (sometimes difficult) questions on-the-fly. These skills are pretty important in academia.

The main purpose is to waste some time. Probably the only thing that does not happen during these meetings is work. Unfortunately, lot of managers and professors think that we need to meet in order to know what everyone else is doing (seen from PhD position). We do meet each other in the coffee room, in the lab, while commuting, after hours, in the elevator and so on. We talk. We know. If we have a problem, we talk. Sorry for the rant, but I had to counterweight all the positivity in other answers.

+1 despite the fact that I disagree with your first 3 sentences, your answer highlight the fact that PIs need to better explain the value of these meetings to lab members.

Check out this old question on how to set up a useful lab meeting, and seeing if any of that can be implemented by your advisor. Maybe you can get some good ideas.

I agree that some labs have meetings that are a waste of time. They waste time because, in my opinion, lab meetings intensify the lab's dynamic. If the PI can't talk to his students like humans outside of a lab meeting, how will he morph into a guiding shepherd for a few hours a week?

While I generally agree with the other answers, I see three additional purposes of group meetings that I cannot accomplish easily in my individual meetings. While the meetings are weekly, I like to have lab members think about the upcoming month.

Notifications about upcoming events: I might tell people about an upcoming conference deadline at our individual meetings, but I often will forget to tell someone.
Management of  shared resources: Getting everyone to briefly say what they are planning to do in the upcoming weeks often highlights that there is going to be high demand for a resource and lets us work out alternative arrangements
Managing my (PIs) time: Maybe this is also a shared resource, but I try and let people know my teaching, marking, reviewing, writing, etc loads. I also try and get people to tell me what they want me to do over the next month. I think this helps people (both myself and lab members) adjust their schedules so that we can tackle tasks efficiently.


text:
If you get stuck in research, at what point in time should you ask for help?
It's always worthwhile to take some time to try to figure it out by yourself. But eventually there's a point where you're unsure how much more time it would take to figure it out by yourself (which could take far longer than you originally think), and when asking for help could be more helpful.
So for analytical or computational research, what are some guidelines for when you should ask for help (from either your adviser, other grad students, or other researchers) when you get stuck?

Related but different (similar question by an undergrad doing research: http://academia.stackexchange.com/q/11914/8966).

I find that grad students always wait too long to ask for help, either out of fear of looking "stupid", or out of inexperience, or out of a misplaced sense of stubbornness. If you've spent a few weeks on something and you're thoroughly stuck, then you should absolutely ask someone (advisor, other students, anyone with knowledge). You'd be surprised at how often you were merely barking up the wrong tree, or just didn't know a very important fact or reference, or just had to reformulate the question differently. All of this takes experience, and that's what an advisor is supposed to provide.

Exactly. In short, "sooner".

This is me in a nutshell. i've been trying to figure out a problem i've had for 3 weeks and i didn't want to look dumb and ask for help, as it seems fairly obvious what i'm supposed to be doing.

All grad students are the same :) (well not really, but in this respect yes)

I think "weeks" is way too long.  There's always a possibility that you are stuck because you don't understand the problem & are working on the wrong thing.  Your time is valuable not only to you but to your supervisor.  I try to have weekly meetings with my students and expect them to post to the group yammer account if they are totally dead stuck for more than 3 days.

@JoannaBryson: that's a fair point. especially if you expect reasonable progress to be achievable in a week, half that time for the "I am stuck" alarm sounds right.

But my supervisor always gets irritated and even angry when I ask him something. He always claims I should do it by myself.

@perfectionm1ng: I was gonna try answer here, then I found your question: http://academia.stackexchange.com/q/11914/8966.

My answer is in two parts.

When to ask other grad students or other researchers for help?

The answer is, anytime. There is nothing to be afraid of asking questions to your office mates, researchers across the doorway or even online. However, they may or may not be able to offer much help because they may not know exactly what you're working on.

When to ask your advisor for help?

The answer is, when you're ready to ask meaningful questions. You don't want your advisor to say why didn't you ask for help sooner. Nor you wanted him to accuse you not working hard enough. If you have meaningful questions and you're stuck for a while - how long is that "a while" usually is a few weeks(long enough to be considered long), you should approach him/her and say you're stuck. Your advisor is there to answer your questions. That's what an advisor is. If you already spend a few weeks on a problem, he would be glad to help you.
You gain more understanding of your research when you try to figure out how to ask questions which make sense because you have to organize your thoughts before asking. Then you're closer to the bottom of it.
However, if you really want to figure it out by yourself for some reasons, you can consider giving yourself a few months. In this case, you would at least let your advisor know you're onto something so that he knows you're making progress. Don't forget he is your advisor. He is on your side !

It took me six months to gather the courage to talk to my research adviser when I was stuck on a project that I knew would "never" work. I should not have waited so long. The conversation we had was very helpful, got me back on track, and, more importantly, got me off the project.
If you are in the same place for more than two or three weeks, its time to have a frank discussion with your research adviser. It's unlikely that he or she knows that you are stuck. The best case scenario is that you have a plan to get unstuck. The worst case scenario is that you are no better off. If you already have a committee, then your next step is to go to the other committee members for help.

It really depends on your advisor's personality, your history of asking for help, the timing of the project, etc. The way in which you ask is also relevant. If you are generally a person who works autonomously and feel you can approach your advisor in a professional (non whiny, non needy) way, most advisors will be happy to help. If you're just afraid to dig in and get your hands dirty (which it sounds you are not), your advisor will probably be less interested in leading you through the process. And there is everything in the middle.
It also depends on whether it's your advisor's project and your project is part of a greater whole; if by delaying too much you are going to slow other people, you should definitely lean on the side of asking for help earlier. However, if you are working on your own idea, you should probably work longer before asking for help. You may also find that you are as much (or more) an expert on the topic than your advisor, so the advisor may not know the answer and may be hoping you'll be the one to figure it out.
There are no general rules. But if you can show that you can figure things out on your own, your advisor may see that as a positive thing and give you a better recommendation for it. On the other hand, if she/he sees you as so stubborn about asking help that you work inefficiently that could be a bad mark.

I do analytical/computational work daily, and I talk to my colleagues quite frequently. Just showing the derivations I made so far to someone often helps me spot my own mistakes, and get new ideas to attack the problem. Your colleagues will often have better understanding of certain subjects that you didn't think would matter for your problem. I guess it depends on your personality (I have highly collaborative), but I would say ask within a day from the moment you got stuck. If someone ends up helping you solve the problem, you will learn from that experience anyways.

"Just showing the derivations I made so far to someone often helps me spot my own mistakes". - Oh yes - that's a very good point!

You should ask whenever you're stuck.  And, as mathematician Peter Sarnak said, "Doing research ... most of the time one is stuck."
You should always be talking to people about what you're working on.  You shouldn't be asking them to solve the problem for you, but you should be asking if they know of relevant techniques that might work on your problem.
You should certainly ask your advisor for help every time you meet with him/her.  Again, don't ask them to solve the problem for you.  Instead, ask whether you should pursue strategy X or technique Y.  This can save you a lot of time (but they might be wrong, too).

+1, but note that not all advisors are amenable to being constantly asked for help. Know your advisor's personality before applying this strategy.

I constantly discuss my work with my colleges all the time,
not only may I get some helpful pointers or references, but asking/staring the question helps me in the solving process, similar to Rubber duck debugging.


text:
Taking into account courses from another university
I think about starting studies towards Master Degree in Computer Science abroad, I finished my bachelor studies few years ago, but I didn't stop studying, during these years I finished few courses of master degree in the domestic university, as result I have transcripts for all of them in English.
The question is what is is the common practice is there any chance that abroad university will consider credit on the courses I already finished, the point is if it's possible I want to lower the pressure to get credit on courses and mostly investing my time in research.
I checked this issue with few another universities in  my country, all of them taking into account the credit I already have with promise to give exemption from studying theses courses if there are requirement of the master degree and to give a credit for all of them.

Each university has different policies, and you should check with individual schools to see if your credit will transfer.  I know the program I graduated from would only allow up to two courses to transfer.

The best answer to this question is Chris Gregg's comment.
You need to check with each individual school or even each individual program.
The schools you already checked with will allow it. Chris's program allowed a maximum of two courses. My graduate program accepted transfer credits infrequently. Some programs may not accept any.

Yes, and it's important to check pretty carefully, since some departmental policies sound much more flexible on paper than they actually are.  For example, the policy may say "we'll award transfer credit if we decide the course is equivalent to our course", without making it clear that they almost never think anyone else's course is similar enough to count as equivalent.

Another factor to consider is how long ago you took those other courses. Some schools are more likely to accept recently-taken courses, but might balk on courses taken, say, over a decade ago.
Also, some schools will want to see an official course description before accepting the transfer credits (or, before letting you use those credits in place of requisite courses in their programs).


text:
master thesis structure
My question is about master thesis structure according to MIT Thesis Format.
I am working on a computer system that comprises of several components. The focus of the research is how to implement the components of the system. Each component can be researched separately. I've implemented all the components and made a progress in improving the performance of some components.
For each of the component I dedicate a section. The question is about an introduction and a conclusion sections. What is the best way to organize them. Should I put a single introduction (about all the components) just after Abstract or separate this big introduction by components and put them in corresponding sections.
The same problem with conclusion.
Sorry for the naive question.

Mosy probably, your thesis is not supposed to read like a collection of unrelated articles. Therefore, you will need one general introduction. It could contain information on

which components exist
how each component is connected to the whole
why components were separated as they are.

This does not preclude additional per-section introductions to explain more in detail what the upcoming section is about.
Proceed analogously for the conclusion and, of course, talk to your supervisor for any specifics.

It wasn't my choice to separate the system into components, it's well-known architecture. One big introduction would look like a several logically separated parts (introduction for each component).

"it's well-known architecture" - then show that you know it well by providing the (correctly chosen part of the!) well-known rationale. Bachelor and Master theses are often different from research papers in that they do not concentrate on findings to a few central questions, but instead also extensively demonstrate your mastery of state-of-the-art techniques that is needed for professionally working in the field.

"One big introduction would (...)" - in that case, increase the abstraction level. Certainly, those components are connected somehow, to fulfil some combined purpose. There must be a reason why they are components of one "computer system", rather than several unrelated projects. To play devil's advocate, your current stance could be interpreted as failure to think beyond your personal task and see things in context, and thus, ultimately, an inability to understand what you are doing. Doesn't your task provide a hint for a common theme across your components?


text:
What are some good questions to ask current graduate students when visiting schools?
For the record, I'm visiting the University of Chicago as an accepted PhD student (in the geophysical sciences) next week.
In particular, I'd especially appreciate creative questions that few other visiting students ask.

see some answers posted in http://academia.stackexchange.com/questions/8507/what-questions-should-one-ask-to-the-former-current-students-of-a-professor-befo

You'll want to get a sense of their feelings for:

The graduate program

Easy to work with regarding customizing the program to their specific needs (i.e., taking courses outside their specific area if necessary)?
How easy/difficult was the process for joining a lab?
Have they found the staff easy/hard to work with?

The advisor

Attitude towards students (respectful/distant/slavedriver)
Presence in the lab (micromanager/occasional presence/absentee)
How organized is the research?

The university as a research institution

Easy collaboration between departments (in their opinion)?
Availability of course offerings (from their experience)?

The city as a place to live

Great answer but it's worth mentioning that assessing "how organised the research is" might be pretty tricky. It's a valuable question, certainly, but also one likely to produce a lot of vague and opinionated answers.

Talk to current graduate students in your lab (even better, working with your potential adviser!)

Ask about their opinion about how the working environment is - what is the working style of your adviser, what is the average time take for a PhD student to graduate from the lab, and where do most of them land up (as eternal postdocs, or tenure-track faculty positions)

What is the funding scenario - do most people have to be TA's for an extended period/all throughout, or whether RA grants are available? What about conferences - do students get funding for traveling to important venues?
What kind of a social life exists in and around the campus, and what is the cost of living - a Ph.D is a long commitment, and you should remember these "soft" criteria as well, so that you are at least prepared mentally when you enter grad school

I'll expand on my answer as and when other points come to my mind!

Few of my favorites are 1) Did anything regarding the school surprise them? 2) Things they wish they had been told when they had visited/started grad school at that school. 3) In retrospect, would they still make the decision to come to that particular school.

I want to add three important questions:

What have you personally done?
What is that you currently work on?
How long have you been here?

The best indicator of future performance is past performance. You are likely to be in these graduate students' position in a couple of years' time. How satisfied will you be if you accomplished as much?