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Advantages or disadvantages of using public repositories for paper writing?
What are pros and cons of using public version control system such as github for writing my papers and reports ?
Is it good to store copies of papers/reports being submitted to conference/journals on such repos. If no, wouldn't it make sense to not use them at the first place itself.

You mean public repositories or private repositories on public service (title and content seems to contradict each other)?

You can keep repositories private, at least on bitbucket. I keep papers/reports in private mercurial repositories on bb. I don't know about github. I don't use it. You wrote "public version control system such as github" You probably meant to write something like "public hosting site such as github".

BTW: See Internet Git repository for collaboration on a paper. In short: BitBucket offers unlimited number of free private repositories for people with academic email. On GitHub (for academic email) still you get a discount or free repos, see https://education.github.com/.

There are a few parts to your question, and I'm not sure which one is most important. If the question is about the value of version control, then you should see the answers to this question (which also has a link to a question about which one to use).
If you're asking about putting it on a shared repository, then here are some reasons:

collaboration with others. If multiple authors are writing a paper, then it's very easy for different authors to edit different portions at the same time without too much worry about conflicts.
portability: I work from different machines, and it's convenient to have a single location to check in/check out from so I don't have to worry about edits on my home machine versus my office machine versus a laptop and so on.

If you're asking about making it public, so anyone can read/edit the paper, then I don't see much of an advantage in that. When the paper is done, it might be handy to be able to download the source of course.

One advantage of using those repositories (in public or private mode) is that you can show the changes and versions of some text. At the same time you can show variations of something through forks. Of course I have no idea why these features might be needed for publication of a paper, but if you are developing a paper collaboratively and you use some text based system, such as Latex, then it makes sense to use those repositories both for source sharing, backup and versioning, and alternative developments through forks. If you want to invite unidentified future authors (probably through fork) then it should be in public, otherwise private versions makes more sense for me.


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How are best reviewer awards given (in a computer science conference)?
I have often seen people(postdoc, etc.) listing in their CV or webpage that they were awarded best reviewer for conference X. I have recently been invited to become a reviewer for a conference, which has made me ponder over what are the criteria for giving such awards? (My field is computer science if that makes a difference.)

I've never heard of a "best reviewer" award so this certainly isn't ubiquitous in computer science. But what makes you think there's any criterion other than, you know, being the best reviewer, in terms of thoroughness and helpfulness?

I am really curious about this: in my field (mathematics), we do not have a separate reviewing system for conference papers (most conferences talks are not directly linked to papers at all; in the ones which are, the papers come after the conference and, if they are refereed, are refereed in the usual way, not by some pre-assigned group of "reviewers").  Is there some small group of reviewers who are all reviewing the same papers (and are qualified to do so? impressive!), so that it makes sense to identify one as "best"?  Very interesting.

@PeteL.Clark You should probably ask a question about how that works since it's too much to explain in a comment. Executive summary: it's organizationally similar to journal refereeing, in that the papers submitted to a journal in any one year will have been reviewed by many different people and ditto the papers submitted to a conference. But it all happens within a month or so, which means that the reviewing is rather superficial.

@David: I see.  Naive question: doesn't that make designating one reviewer "best" a bit unfair (everyone is reviewing different stuff)?

@PeteL.Clark No more unfair than designating one paper "best", given that everyone was writing different stuff? But, as I say, I've never come across a "best reviewer" award so I'm winging it only slightly less than you are, here.

BPM (http://bpm-conference.org/BpmConference/) has a best reviewer award AFAIK. It is a simple vote by paper authors (i.e., every author is asked for feedback on the value of Review 1, 2, 3). I am not sure how far this is away from entirely random, as I presume that authors of rejected papers are typically not satisfied with their reviews, but authors of accepted papers are. Anyway, a friend of mine got this award two years ago, and he does write very thorough conference reviews.

I have no concrete criteria (that's why not a response), but anecdotally, I know that it is being awarded to particularly knowledgeable reviews or reviews into which particular care at various levels has been invested.

Here are the criteria used by the ACM 2012 International Conference on Multimedia Retrieval (ICMR) for the "best reviewer" award:

The criteria are that the reviewer should have demonstrated the expertise to provide insightful and knowledgeable feedback, should have provided quality reviews which are helpful to the authors of papers, should have displayed collegiality and constructive feedback, and should have completed reviews on time. The award is selected after examining all of the 400+ reviews from the 101 reviewers.

Conferences with an author response phase may use the authors' replies to help choose the best reviewer. For example, the CFP for the 2014 Conference on Software Language Engineering says:

Authors will be given a brief opportunity for a reply to the reviews. The replies will be considered in the PC's discussions, and considered in the selection of the best reviewer.

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What does "university ranking" mean for a graduate admissions committee?
Many questions on this website ask how university rankings affect the future career in research and graduate admissions. But it is not clear for me what is actually meant by ranking. There are various rankings of universities and many of them are contradictory.
Thus, in the context of graduate admissions what ranking does the admission committee have in their mind? How does the committee decide which is a high-ranked school and which is a low-ranked school?

For larger graduate programs: School X is ranked higher than School Y if past students from School X have been more successful than past students from School Y.

Paraphrasing A. Tanenbaum, "The nice thing about rankings is that there are so many of them to choose from".

@JeffE And how are they defining success? Salary? Number of people managed? Subjective happiness?

Probably "success" = "effective progress through grad school"

In the context of graduate admissions, the “ranking” of universities by members of the committee is a purely subjective one, and depends heavily from place to place, from department to department, and from committee member to committee member. That's why you're not getting a simple silver-bullet answer to your question.
Now, most admission committee members will rather rely on their own past experience with students coming from various schools, and would probably go further and would not “rank” the same the different undergrad programs from a given university. They would typically consider things like:

how ready were past students from program X for our graduate courses? e.g., did they know and master well enough all the prerequisites for our courses
how well did these students do during courses? e.g. what sort of grades do they get (knowing that a top student from school X usually doesn't make it to the first half of your program, for example, is interesting to know for future candidates from this school)
how well did they perform in terms of research? e.g. school Y has students with excellent grades and educational record, but are they prepared for a wide-ranging professional experience that is a PhD?

(I speak for a mathematics grad program and admissions...) In any case, it's not literal "ranking" that is generated by some for-profit group, but, rather, not-so-young-anymore faculty peoples' knowledge of the relative rigor and standards of a program, and the appreciation (or lack thereof) of that faculty's conception and awareness of what graduate programs demand of students. Of course, yes, some faculty have arrived at modest places by choice or by chance after times spent at "high-status/tier" places, so have an idea about the larger world, so their appraisals of the potential success of their students carries more weight. Yes, obviously, some faculty at lower-tier places have less idea of the rigors of "fancier" places, so give dubious opinions about future success of their students. It is more plausible to imagine that faculty at higher-tier places are aware of how their own graduate program works, at least, and can imagine the success-or-not of their undergrad proteges in comparable programs.
In summary, it's not really about "status/ranking" per se, but about "demands of the program", and expectations for PhD projects and coursework background.
In particular, it is not the case that while looking at grad applications, I automatically think applicants from higher-tier schools are better... What does tend to be the case is that there's less volatility in the letters-of-recommendation from such places, since the faculty have more substantial track records (regardless of whether they're big-shots), and can speak more convincingly about probable success of their students in our program.
For applicants from small colleges, etc, it is indeed a bit harder to gauge potential, because they may not yet have been challenged, by coursework or projects. (Many or most "REU"s are of interest, but don't at all reliably "stress" participants, and this is by design, presumably...) Not a moral failing, for sure, but not so useful in gauging potential for future success in a less jolly, more stressful, environment. But, duh, admissions committees realize that not all mathematically talented people happen to go to colleges/universities where the faculty are able, or inclined, or allowed (!) to stress them. And maybe the available courses are limited, for various reasons.

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Can a masters student apply for a second masters in the same field at another university?
Are students with masters degree allowed to enter a masters program in the same area at a good university?
Is second masters a good option for a better research experience and improving your CV before applying to a PhD in top programs? I am specifically interested in US universities and computer science.

Many universities don't allow new students into degree programs where they already have a degree (i.e., you can't get a Master's in the same field in which you already have your Master's), but I imagine it is on a case-by-case basis if you don't have your degree yet.

In what country? In France, for example, there is nothing to stop you from obtaining a second Masters degree in the same field if you want to…

I'm mainly interested in US.

I can't say anything about the US, but in many countries you can't get a 2nd degree in that same specific subject, but since there are plenty of specialization masters in CS (AI, Game Design, HCI, Software engineering, Web Engineering) you can obviously choose one of those.

Every university is different.  But for most universities in the US, the answer is probably no.

Getting a second masters degree in the same field may be allowed, but it's extremely rare and I don't think it's a good use of time. I don't think it will help you get admitted to a PhD program. It would just look like an anomaly to the admissions committee. I think it would make more sense to apply directly to PhD programs.

But most PhD programs require significant research experience, preferring candidates with multiple publications. How would you suggest getting that experience if the person has already graduated from a (taught) Master's program?

@SilentStone: "But most PhD programs require significant research experience": this is not necessarily the case and is definitely field dependent.

I'm doing a 2nd Master's right now in Philosophy when my first was Philosophy of Religion (same classes basically). Both schools are American. There are some schools that are often recommended for people trying to get a 2nd MA in Philosophy. You most certainly CAN do it, at least in the humanities, although there are some cons to going about things this way.

But was the 1st MA say the one at Yale in Divinity and the second MA from a humanities program?

You are certainly allowed to apply, but your chances of getting accepted for a second master's in the same field is approximately zero--with one exception.
If you already have the master's degree you're seeking, most graduate schools will assume that you are really applying for a doctoral program, if the degrees are awarded separately. If you make if clear you are applying for a second master's degree, they'll probably just throw out your application.
The exception to this are programs where you can only be admitted as a doctoral candidate, but can earn a master's along the way. Then the normal procedures will likely still apply. Otherwise, you're out of luck.

What if the second MS is in slightly different field? For example the first MS is in CS and the second MS is in Quantum Information Theory?

I don't think CS and Quantum Information Theory would fall into the "slightly different" category. Good example of that  would be CS and CE.

@AbrahamGuchi So CS and QIT will be considered same?

If they're offered by the same department, usually.

It varies by university. I was a computer science PhD student from 2002 to 2009. If I had dropped out, I would not have been awarded a master's degree because I already had one, awarded in 1975. The changes in computer science between 1975 and 2002 were apparently not enough to make it a different subject.

Besides to very good advices posted in other answers to this question; I want to mention a few words.

Can a masters student apply for a second masters in the same field at
  another university?

I think, you are asking about applying and then studying for a second same masters degree. Because a student may be free to apply for a degree, but the admissions office will reject his profile as he is currently student else where.
Answer to your question depends on the educational system of the country and universities policies too.
In some countries, studying simultaneously in two universities and majors is prohibited and graduate students are only allowed to study in their own university. Also, I have seen many universities asking students whether they are currently students or not, because they seek full time students not part time ones.
However, I have seen that some students with outstanding grades and educational background can apply a minor very close to their field in their own university but it was for bachelors level only.
Also, you may find a university which accepts students seeking for double major; but the university in which you are currently studying may not agree to you to study a second major when you are their students.
As a general advice, double check the regulations of both universities and the countries in which you want to study simultaneously.

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Indicating a name change after publication
My wife has publications under both her maiden name and her married name. How should she indicate that this is the case on her CV, if she wants to mention publications from both time periods?

Jane S. Doe (also known as Jane Smith). I saw this kind of names on CV. Any other ideas?

@scaaahu We saw that you can use "nee [maiden name]", but idk if that's internationally understood or just an American thing.

@Tacroy Speaking as someone from Britain, I'm familiar with née. You can find it on gravestones here.

It may be too late, if she's already published under both names, but one solution is just keep publishing under her maiden name (they don't check your driver's license when you submit an article).  This has its own possibilities for confusion (as does changing your name, as does keeping it), but certainly has been done.

I know 2 female professors personally who clarify this fact very similarly. What they do is this:

They cite the relevant publications as they were with her maiden name and her new last name.
They add a * at the beginning of the "Publications" section in their CV which refers to a footnote to that page which then says something like this "* Last name changed to Smith from Doe in 1988"

That seems to work very well so far.

A short answer, I think one can write

"full present name", born "maiden name"

or

"full present name", formerly "maiden name"

and put this in the top of the CV where you have personal details and/or also as a subheading for the publications list.
I also bold face my name in all publications, This way it should not pass anyone where I am in the publications list.

It's somewhat archaic and may have problems if people don't know what it is, but for brevity and specificity it would be hard to beat "Jane Smith, née Doe"

I am in this situation, too. I site my publications as they appear on PubMed, keeping the outdated last name where it is seen on the original aricles. I then underline my full name in each publication, whether it is the current or former last name, i.e. "Jane M. Doe" and "Jane M. Smith" would be underlined in the Publications section. I also have my full, current name at the top of my CV/Resume (i.e. Jane M. Smith) so it is clear that the underlined person (whether Doe or Smith) is me. I have had job coaches indicate they like this strategy.

Unique ID services for authors like ORCID (http://orcid.org/; non-profit) and ResearcherID (http://www.researcherid.com/; associated with Web of Knowledge) are the way to go. You can list all your previous names on your ORCID profile, as well as alternate spellings. Many publishers (including Nature, PLOS, etc) and funders (both in the US and elsewhere) are starting to use ORCID to help manage authors' identities. ORCID suggests placing your ID prominently on your website, CV, and anywhere else folks might encounter your professional identity, to help with name disambiguation.

This doesn't seem to answer the question, which is how should Jane Doe indicate on her CV that the publications listed with author Jane Smith are also hers? People reading a CV aren't going to want to find some website and type an identifier into it.


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Concerns about the value of the research domain
I am a PhD student in applied computer science methods, halfway through the program, and the question that is in the title is what have occupied my mind almost from the beginning of my study. I can't find much help from my supervisors, and this is putting the whole pursuit of my degree under question.
I have read some literature in the domain of my research, and most of the time my critical thinking is not satisfied with what the authors have achieved in the end of their work. Somehow, the conclusions do not seem convincing to me. In my understanding, the idea of a scientific article is to be useful, but what I see in my field of applicational studies is that the articles suggest no real applications, rather some dull scientific examples, saying that it demonstrates its usefullness. Applicational studies should have real applications, not examples in a vacuum.
And it is the same thing, if not worse, in almost all the articles. It gets worse if they start to overcomplicate things, adding one method on top of another to achieve no evident benefit at the end. For me, such research seems like they cannot find a good problem.
Is it just an impression of a sceptic, or could it be that my subfield of research has reached the point where it has closed on itself? I mean, producing papers not to investigate real problems, but just to keep the field afloat, although it has no potential for anything innovative.
I am just starting to doubt that research itself has some special value, as it seemed to me in my idealistic view when I just started my PhD. At this point, I am overwhelmed with the thought that the years that I am spending on my PhD eventually will result with a similar contribution: It will have no use or value. Maybe except to support my supervisor's career and add to the mess of the literature of my domain, where I already have sunk.
So my question for you is: What does motivate you or give you certitude that the things that you work on do have impact, and the work is worth working on?

Did it cross your mind that it might be problem of your adviser and how s/he guides you, rather than of the research domain itself?

I cannot possibly agree with the currently most upvoted answer by Pete L. Clark. I clearly cannot comment on the particular subfield that OP is asking about since I know nothing about it.
However, daily I see stillborn research papers --- they were conceived not to dispel the ignorance, but to be added to a CV. There are definitely research communities that are mired in posturing, complexity and obscurantism.
On a personal level, it does not matter whether the field in question is one such area, or whether the OP lacks the background to see how this field adds to our knowledge. It is impossible to do good research without seeing the goal. So, action is necessary.
I suggest talking to the advisor, and gently asking these questions. If the answers are not enlightening, change field/advisor. Doing otherwise is a waste of OP's time.

"However, daily I see stillborn research papers --- they were conceived not to dispel the ignorance, but to be added to a CV." Yes, I have seen bad papers too...but these are not the ones a graduate student should be studying.  "There are definitely research communities that are mired in posturing, complexity and obscurantism." To the extent that there is no progress being made at all?  I haven't.  Part of me is tempted to say that whether a community is mired in p, c, and o is in fact rather subjective, and this may be a way of saying you don't like them....

...But doubtless there is more on academia and earth than is dreamt of in my philosophy.  (I am tempted to ask both you and JeffE for a specific example of a "bad academic field," but I don't think it's really appropriate to do so.)

@PeteL.Clark: I refer you to Sturgeon's Law. I don't see why academia should be any different. And there are a lot of rubbish papers out there, often stemming from the whole "publish and perish" thing. There's a big industry whose justification is churning out research activity, even when it is of little or no value.

@Faheem: I am certainly not saying that X% of papers in an academic field are important or valid or meaningful or whatever.  But it is different to say that an entire academic field is without value -- why is a group of intelligent, well-trained people devoting their professional lives to something that is without value?  It would seem evident that the practitioners of the field value it, and to my knowledge all academic fields have representatives at the world's top universities, who have their pick of the litter -- why would they hire people who are doing useless things?

@PeteL.Clark The "area" of research is defined subjectively by each researcher. Empirically, there is an inverse correlation between competence of researcher and how wide the self-defined area is. So, looking from the top, you might see a few dozen areas, each of which is represented in world's best universities. Looking from the bottom, one sees many thousands of areas.

In my understanding the idea of a scientific article is to be useful[.]

That is not my understanding of a scientific article (or, more basically, of science).  Science is a growing body of knowledge and understanding achieved by a characteristic method, and a scientific article adds to this knowledge and understanding.  (Roughly; scientific articles can also critique or falsify...)  Who said it had to be useful?  It is always more useful to have scientific knowledge than not to have it, and many branches of science are easily applied, but by no means all: e.g. up until relatively recently it was believed but not observed that there were exoplanets, i.e., planets outside our own solar system. The first confirmed detection of an exoplanet was in 1992.  This was surely one of the major events in the history of astronomy, but...what is it useful for?  Something big a thousand years from now maybe, but nothing now.

I have read some literature in the domain of my research, and almost always my critical thinking is not satisfied with what the authors have achieved in the end of their work. Somehow the conclusions seems for me not convincing.

To be honest, I am skeptical of this.  Academic fields are built by intelligent, serious, hard-working people, often over the course of several lifetimes.  What counts as methodological rigor in one academic field may not in another, but that's not the same thing.  If as a mid-career grad student you find that most of the papers you are reading are pointless and limited in a way that you think you see through...anything is possible, but I am going to guess that you are missing something.

Is it just an impression of a sceptic or it could be that my subfield of research has reached the point where it has closed on itself (producing papers not to investingate real problems but just to keep the field afloat alrhough it has no potential for anything innovative)?

I have not in my lifetime met a scientific (or other academic) field where the grad students can tell that nothing deep is going on.  It is true that different fields at different times progress in different ways: periods of fundamental advances alternate with periods of more modest improvements and aggregation of knowledge.  But they all survive.
To me it sounds like you are just not intellectually interested in your academic field (or the sub-sub-... part of it you're currently occupied).  You write:

I am just starting to doubt that research itself has some special value, as it seemed to me in my idealistic view when I just started my PhD. At this point I am overwhelmed with the thought that the years that I am spending on my PhD eventually will result with a similar contribution, there will be no use or value of which. May be except to support my supervisor's career and add to the mess of the literature of my domain where I already have sunk.

In my experience, younger students tend to idealize and elevate academic research as though it were something sacred.  When I was a young student of mathematics, I explained why I liked mathematics in terms of its objectivity, its timelessness, and so forth.  I don't say much of that anymore -- and not really because I don't believe it: I still do.  But I don't believe that it explains why I did mathematics, because the explanation is not enough.  There is a lot of mathematics out there; I try to appreciate all of it, but I don't do all of it.  Obviously I did not become a number theorist rather than a differential geometer because number theory is more objective or timeless -- or useful! -- than differential geometry.  I became a number theorist because I like (and understand, and have a proclivity for) number theory more than differential geometry.  There's an ineffability there that we may as well be honest about.
I hope you see the point of that personal digression: I suspect that you simply are not interested in your subfield of applied CS and are therefore searching for more sweeping intellectual explanations of that.  But you don't need to -- if you don't like it, you don't like it, and that has to be respected, in particular by you.  No, you should not continue in a field just to bolster your supervisor's research career.  So it's probably time for a change: whether a small change or a big change I leave up to you, but an intellectual defense of the value of Academic Field X is almost certainly not the answer.
Good luck.

To be honest, I am skeptical of this — Having read many unconvincing computer science papers, I am not skeptical.  At all. — I have not in my lifetime met a... field where the grad students can tell that nothing deep is going on. — I have.

Agree with @JeffE's comment. I think we could point to the many fields that have a replicability crisis, for example.

I think your answer portraits a generally too optimistic view: it's true that academic fields are built by intelligent, serious, hard-working people, but it is also true that there are a number of fields (I can name a couple) that are so close in themselves to prevent any real progress.

@Massimo: It may well be so.  I think you probably know me well enough to know that I am not generally too optimistic, so if I am too optimistic once in a while, maybe it all balances out. :)

"That's why it's always worth having a few philosophers around the place. One minute it's all is Truth Beauty and is Beauty Truth, and Does a Falling Tree in the Forest Make a Sound if There's No one There to Hear It, and then just when you think they're going to start dribbling one of 'em says, Incidentally, putting a thirty-foot parabolic reflector on a high place to shoot the rays of the sun at an enemy's ships would be a very interesting demonstration of optical principles..." -- Terry Pratchett, Small Gods (Discworld) (1992)
"The release of atomic power has changed everything except our way of thinking ... the solution to this problem lies in the heart of mankind. If only I had known, I should have become a watchmaker." -- Albert Einstein (1945)
"No one has yet discovered any warlike purpose to be served by the theory of numbers or relativity, and it seems unlikely that anyone will do so for many years." -- G.H. Hardy, A Mathematician's Apology (1941)

This is the fundamental conundrum of doing research. You hope that the research you are doing will revolutionize the world, and write grant proposals to that effect, but it's really a crapshoot. Maybe you'll hit a breakthrough; maybe your contributions will languish forgotten on shelves. Maybe someday your works will be dusted off when it is realized that they are exactly what is needed to advance humanity. You just don't know; "practical" applications are usually years off at best.
So what are you supposed to do in the meantime? In my experience, it has to be a question of extrinsic versus intrinsic motivation. Presumably you were excited about your field when you started your PhD. You decided to devote years of your life to the study of a single subject...why? Mathematicians worked on number theory for hundreds of years before RSA and SHA; Einstein never saw photovoltaic solar panels in wide use; Alan Turing never wrote a single program in C++, Java, Haskell, or Python. What kept them going?

I wonder: Should the fact that the field in question is applied computer science change anything about this answer? That is: the OP got into the field precisely because of the promise of applications, right now, actually baked into the name of the particular discipline?

@DanielR.Collins In principle, yes--there should be more of an applied eye. But it's still fundamental research. All that really changes is that the "time to market" might decrease from decades to years. I felt like the other answers addressed some practical concerns (networking, changing fields, writing your papers in a certain style, etc), so it was necessary to address the motivation for doing "theoretical research" even if it is within an "applied field."

wow this Hardy quote is so out of context, it's not even funny anymore. you present it as if hardy was complaining, while he was in fact proud that number theory lacked applications in warfare.

@Rüdiger Absolutely; So if there were no applications for number theory, why would he even bother doing research? That is the point I'm trying to make. Hardy's whole argument is not that number theory is useless and we should stop working on it; rather it is that number theory is the queen of mathematics, regardless of what applications may come up.

It will have no use or value. Maybe except to support my supervisor's
  career...

I have seen that happen many times. It won't be too terrible if it happens again in your case. Not many people get lucky to hit the bull's eye in their PhD program. Most learn how to do research researching something that turns out to be irrelevant. They publish a paper or two that few people will ever read and get their degree. The real result is the research skills that you will use a lot and improve throughout your career. I would just go with it and try to make the best out of it.

Having worked in an applied algorithmic field as well, I fully understand the problems of the OP. My experiences:

Many "applied" papers are not applied in the sense that they consider problems that are asked in the "real world". They may be modelled on real world problems, but in such an abstract way that you cannot use the results to e.g. implement them into some practical useful software. "Applied" is a very wide range.
Most research areas are driven by peer review. If a group of people like an approach, this approach will survive and more papers are produced in this direction. This includes the danger of overestimating the value of a certain method or drawing questionable answers from inconclusive data. Nonreproducible results on many experimental fields often result from overconfident use of statistics.
Many grad students work pretty much on their own and therefore have difficulties to distinguish good from bad papers -- the bad ones are just too many.

Nevertheless, there is progress in nearly every field of science, but -- in my opinion -- it can be buried in a large amount of fairly disappointing papers.

@Pete L. Clark gives you a great answer that, I believe, helps you to see where you are and where you may want go.
In case you're still holding ground on what you think about your field, then I suggest you to see that as an opportunity to do better than the others around, to bring new things to your field. Try to answer this: what can I do to advance the research in my field? If you are certain that the current research is poor, then you are seeing its flaws and you have a good chance to give great contribution.

@Saturnus I think I was distracted when I first read your comment in the question. I read it as you were criticizing the OP. Now I see that I agree with you. Thanks for making your point here too.

I will add a somewhat optimistic answer.
There are a lot of "bad" papers written, in every field; those which are poorly constructed, those with errors, those struggling to find a reason to exist, those published to pad someone's CV, those published for political reasons, etc.
However, think of research as a creative pursuit. Do you think that music or art is not worth it, even though most of it is "bad"? Most of it is trying something that won't work, or it's copying someone else, or it's boring, or it's unclear. Once in a while, something truly special comes along, though; to some people, that's worth it.
As a researcher, you need to learn to separate the good ideas from the bad - there are good papers out there, I promise you. It's likely that many of these bad papers you're reading cite them; follow the citations back. Find the gems and study those hard.
Finally, you can tell that most of what you're reading is bad, which implies that you can tell what is good. Take advantage of that skill!

This is a common view on first getting really stuck in to the literature, when you realise just how small the increments by which we actually work can be.
You've started to see your own work in the same light.  That's normal too.  But very few theses are actually a significant contribution to human knowledge.  By the end of your PhD, the world will have one more computer scientist -- you -- who will be able to work on a wide range of problems, even if a small part of any of them.
Note that unlike some answers I make the perhaps unrealistic assumption of good faith.  The only effect of the pressure to publish frequently is to exaggerate the incremental nature of progress -- but then the results are out there sooner for others to build on.

When I was studying math, discussion was made of pure and applied mathematics. To top-notch pure mathematics culture, it is almost a matter of pride to create research not used in applied math, and a loss of honor, so to speak, if an applied mathematician finds a practical use for your research.
One point which was underscored repeatedly was that not only is applied math finding uses for the most esoteric math you can find, but the time lag between pure math discovery and applied math application was shrinking, and something like 2-3 decades as of the years of my program.
People have come up with examples of mathematical research that is so obscure it will never be applied; one such prominent example is group theory, and I remember it being all the more striking when a friend studying chemistry referred to "the group of rotations of a molecule." She was using the term correctly, it was properly an application of group theory, and it was concrete enough to be used in this way by (nonmathematician) scientists.
Make your computer science work as obscure as you like, but it will probably end up seeing practical use.

If your applied field isn't applicable to the real world, the least it could do is change its name. It's also possible that that path of research is a dead end - it wouldn't be the first time in human history that people went the wrong way intellectually.
What would a research domain gone wrong look like? Probably as you describe - the next generation loses faith and questions whether to abandon it. It's possible you're correct and you're at the forefront of this point, another possibility is you could be wrong and just don't get the field. I don't know.
Be true to yourself and be aware of both the sunk cost fallacy and the fact that you have sunk some costs. Depending on how much time you've spent, and whether you can switch to a different topic, you may want to finish and grab the credentials. You'll be a much more formidable critic of the field once you achieve that, but of course by then maybe you'll believe it, whether it's true or not :)


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How to start writing a literature review?
I have 2 months where I should write the literature review for my PhD thesis. However, I don't know how to write one.
In general terms, what would be a good way to start the literature review? For instance, how can I organize the reading and divide it in topics?
I would appreciate any helpful ideas, books, or articles.

This doesn't have enough specific information (what's the project, what's the field, etc.) to actually yield meaningful answers.

+1 More context relevance is needed to get specific answers.

You should organize your reading according to logical subtopics, which will only reveal themselves after you start reading, or maybe only after you start writing.  Stop worrying about how to do it right and just start.

Didn't you have a research methods class where you learned how to write a literature review?

Since you don't say what field you are in, this may not work for you - but I'll describe how I do a literature review in the biomedical sciences. I've tried to be general, so it could apply to other fields, but if you're not in science at all it might not work for you.
The first step to writing a literature review is defining your topic. What is the key question/ concept you are trying to explain or summarize? This can be difficult if you are really starting from zero on a topic, and will probably need to be refined as you work on your review. But it's important to define this at least in draft form before you start.
The second step is coming up with search terms. Begin by searching your question/ concept on Google Scholar or another large database - if it's a biomedical topic, Cochrane Reviews is a good place to start. I'm not sure if there are similar review databases for other fields. Look for a few key papers in the area, read those, and look at their reference lists. Also, record their 'key terms' (usually below the abstract) - these will help you define search terms. Pull relevant papers from their reference lists and repeat. Once you've gone through ~ 10 papers you will probably have a good sense of the type of key words that are important for your topic. Use these terms to build an improved literature search.
Third, you need to actually do the literature search. Your field probably has a database of journals - use this and your search terms to identify all relevant papers over whatever time frame you are interested. You'll probably need to refine as you go, so you don't get swamped with papers. I prefer to go use a systematic search strategy, even if I'm not doing a systematic review, since this removes some subjectivity. This means going through all results, and reading any papers which have titles or abstracts that suggest they may be relevant to your question.
Fourth, you need to read and take notes. Make sure your notes are indexed by paper, so that you always have the citation of the original paper with whatever facts you note down. I find OneNote is a great way to do this, but there are other tools I'm sure.
For me, once I've read 20 or so papers, I usually have a pretty good idea of what the answer to my question/topic is, and what the nuances are. Then it's just a matter of organizing the notes that I've already taken into a rough outline of what I want to say (remembering to keep label all the facts/opinions with their citations). After that, you're ready to start writing, and it's not too difficult since you've already got a good sense of what to write as well as a rough draft in the form of notes.
One important caveat is that you should always re-write all your notes in your own words as you go through the outline converting it into a paper. This way, if you occasionally just copied the original author's text when taking notes, you won't end up with their words in your paper (which would be plagiarizing).

What a great explanation. Thank you so much, if you just can add: what should I do exactly after I paraphrasing the notes? Should I add any comments? or compare and contrast or disagree,etc?

I usually use the notes to construct an outline of the paper, and then flesh it out with your own thoughts or conclusions. You'll probably want to provide evidence supporting your general arguments, and evidence against your arguments with reasons/evidence why you think they are incorrect or don't apply. Comparing and contrasting is usually good, but may be a bit more topic specific. In general, writing is where things get more field/topic specific, so it might help if you can give me a general idea of the subject area.

Depending on your topic, I recommend that you start taking the basics from books. After that you can get more specialized information from articles or journals. Do not forget to keep a list of the references that you are obtaining, maybe with a little summary of each of one.
Another advice is that you start writing about the information that you get, then cluster your information by similar sub topics, so you avoid the formation of information islands.
Good luck!


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How much patience is needed in a PhD?
I am a PhD student who works in theory. I have been patient but nowadays I am losing my temper, patience, etc. Many publications have been rejected as well as my proposals for grants. I have submitted one research paper which was also recently rejected.
I am working very hard but also feeling disheartened about the way academia works. As a student it is very hard to be patient. I worry each time my proposals get rejected or even if I have a failure in my research. I am trying my best to be patient but I don't know how to keep it.
Question:  How much patience is needed while working on a PhD? (in terms of number of years for a publication) Is there any way to not worry about the failures we have in academia?

This will continue after your PhD as well if you stay in academia. Everything we do is subject to critical evaluation. It has to be. But that also means we get a lot of criticism and rejections. We should do that constructively, but not everybody is equally good at that. So what you describe is pretty much a permanent state in academia. Best thing you can do is not identify too much with your work, so you can treat it as criticism of your work and not as criticism of you (even when it was incorrectly formulated in such a way).

Question: How much patience is needed in PhD? Answer: Yes.

How much patience is needed in PhD? -- Unless there is a way to quantify patience, I don't think this question is answerable in its current form.

28.7 kiloGhandis.

infinitely much

Highly relevant: https://academia.stackexchange.com/questions/2219/how-should-i-deal-with-discouragement-as-a-graduate-student

The PhD is a test of your stubbornness, patience and grit more than it is a test of any sort of intelligence or ability.

Benjamin Franklin is said to have said "I haven't failed. I've found 10,000 things that don't work." It is all in the question of how you frame things. Abstract mathematics is not one of those publish-30-papers-a-year fields. It can take a horribly long time until you finally see how to solve your problem, and then you can't un-see it anymore and you wonder why you were being so silly about this for the past x-years. Just keep at it, find one more thing every day that doesn't work, and make sure to do something that is NOT mathematics every day.
As noted by Ian Sudbery above, the PhD just means you were able to convince a committee of busy professors that the complete sentences/experiments/proofs you have bound between two covers is an original contribution to your field.
Also, http://phdcomics.com/ helps. Daily. Read all the back strips, too.

Benjamin Franklin? :O I thought that was Thomas Edison, in reference to lightbulb filaments...

Theorem: Every quote found on the Internet and on calendars and at the beginning of book chapters is attributed to at least 5 different people because no one bothers to check the sources.

As previously discussed we cannot answer your question, as we cannot quantify patience.
But I really wanted to add another measure for you. Not saying you don't need patience (you need it, a lot, generally in life).
But what about resilience?
I would strongly advise you to think about fostering your resilience. It feels less hopeless and helpless than patience. But in the end, patience is probably a part of it. Further discussions of this would most likely be more in the scope of Philosophy.SE.

As user Mad Jack already pointed out above in the comments section, it is very difficult to quantify patience. I can only speak from my own experience and will say that you do need inordinate amounts of patience and as much patience as you need to last you through the journey. Publication rejection is extremely common - in fact - (given the acceptance rates of journals) - is the norm rather than the exception.
You cannot 'don't worry about failure' - you will! You just have to get used to failure and celebrate your wins. Know that it comes with the job of being a Phd student and in academic generally.

abaa:

Personally, I think less patience is more often the guidance I would give rather than more.  (Because people waste time.)  That said, given your situation, I would say "hang in there".  Once you are part way down the road, it is just better to finish it.
My advice on publications is to

a.  Aim for "decent" but not premier outlets.  (Unless you have a momentous discovery.)  I don't know math, but in chemistry, I would say pass on Science/Nature.  Pass on JACS.  Go for specialized ACS journals or the equivalent (Inorganic Chemistry, Chemistry of Materials, etc.).  [There are several layers lower. But you are at a decent level in the subfield.]
b. Be very honest.  And don't try to be fancier than what you are (leave that for grant proposals).  I have several "no revisions" papers.  My advisor, with 30+ students and a couple hundred papers (and 400 as an editor) had ZERO.  But the reason, I got them was I was brutally honest.  Drop a sample on the floor...no problem.  Report it. AND my work wasn't even textbook.  In some cases, I just needed to write up what I had and (as usually happened), the experiment design was not perfect.  But I had something.  And I wrote it up.  and was brutally honest.
c.  Follow all the requirements of the submitting journal (exact format for references, etc. etc.).  Usually the January edition of the journal will have instructions for authors.  Follow them with a NUCLEAR emphasis (checking every single detail.)
d. If you want some motivation/explanation, read the NASA pamphlet by Katzoff or the relevant chapters in E Bright Wilson "On Research" (look them up...will mean more when you do.)

Good luck and look out for yourself.

I think you just accidentally(?) claimed your adviser wasn't very honest on his papers...

What is at the core of what you described?  From what you wrote, I'm imagining you getting irascible with friends and colleagues, and sometimes feeling desperate within yourself.  Is that the case?  What I wrote is based on observations about myself in a time of great stress, and also on my spouse's description of feelings and behavior during the last stretch of the PhD.
I wonder what percentage of the feeling of impatience you're having comes from anxiety.  Anxiety that your hard work won't be recognized, anxiety that this period of your life will feel ever more endless, anxiety that the way you're feeling and behaving will cause irreparable damage to your relationships, or even to your way of relating to people in general.
Well, facing up to one's fears is never enough, is it?  Why I'm asking: when one realizes that anxiety is making it extremely difficult to function effectively, then it is time to tell others about it.  I don't know if that's the case for you, but if it is, then please do.  Tell people.

The key is "Staying-Alive".  Good research, getting published, getting degree, getting noticed.... all those things are great, but these things (at least for most of us) comes after failures, rejections, frustrations  and all the bad things we don't want.  However, you need to satay live for it to come.  It will come, so stay alive until then.  Don't loose it.
It is like going through a long tunnel with so many doors - working hard to reach a door thinking this is it, but it only opens to another distance with another door at the end.  But, if you stay alive, you will reach the door with the sign "PhD" on it.
So, breath in and breath out, and stay alive.
But, I may warn you - you will have scars all over you.  Until now, if I have a bad dream, it is about those days in research.  It wakes me up in the middle of night with cold sweat all over me.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Who is the copyright holder of a PhD thesis published in ProQuest?
I have a Ph.D thesis obtained from ProQuest. I would like to reuse some of the figures from it in my own work.
Every page of the PDF contains this message on the bottom:

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission.

How can I find out who is the copyright owner? It is not listed anywhere in the PDF, and I can find nothing useful on ProQuest's website.
The thesis is from the 70s, and the author has not been academically active since then. Tracking him down seems unlikely.

An uneducated guess: the writer of the thesis still holds the copyright. Even if not, she/he is your source for a similar figure that can be shared with permission.

@Greg - see my edit.

This is unfortunate. Can you contact the university, maybe they have a policy about copyrights of PhDs that people wrote there...

The original author is probably the copyright holder.
Two other options: it is possible that it is the university/research institute (see, eg, this MIT policy for an example) but this is relatively unusual; alternatively, if it was done with industrial sponsorship, the company might own copyright. If either were the case, though, I'd expect to see some kind of indication on the thesis itself. Absent a clear hint (eg an existing university policy, a commercial-looking funder) that someone else would hold copyright, I'd work on the assumption it's the author.
You can try and trace them - this is not quite as impossible as it sounds, as the university alumni office may well have contact with them and be able to pass on a letter. If you have tried and failed, you might still have the option of using them without permission and an apologetic footnote...


text:
Can a Ph.D. student visit another lab for a week to learn a specific skill/topic? (inside EU)
I am wondering if (and how) a Ph.D. student could learn a skill that is the area of expertise of another lab inside the European Union, but in a different country than the university on which the Ph.D programme is currently done.
So lets say my lab does not have any experience in X procedure. I know that university in another country inside the EU has expertise in X.
Learning the basics in X takes about a week of hands-on lab experience.
How could I initiate the conversation between universities to get me to the other lab? is this even necessary as I would not be paid for that week while visiting the other lab?
Or do I only need to get the permission of the lab supervisors and do not bother about the paperwork.
I am willing  to commit to travel and accommodation expenses from my own budget.

Start by asking your supervisor or if they are not very helpful - some other member of staff who's supposed to look after you (second supervisor, PhD tutor, etc). I think, spending time in another institution is a common practice. I know a few people who did what you're talking about, but I don't know how things were arranged. I'd expect that your Uni should cover some reasonable amount of travel, but you'll need to pay accommodation from your PhD salary or stipend in you receive one.

Hosting another researcher is not a lot of trouble, assuming the lab doesn't require any high biosafety credentials. The host needs to provide access, consumables, and some space. The bulk of the paperwork would be done by the host, as they know what they need.
The usual procedure for PhD students is for your professor to talk with them, but you seem to be an established researcher, so if you know them you may ask them yourself. Remember that for them, their biggest commitment is the time to actually train you, so you have to somehow make it worth their while. You could offer an exchange or a collaboration, for example.
If the procedure is of sufficiently wide interest, you may convince them to organise a school and train several people at the same time, for a fee (in computational subjects, where we don't have to pay for reagents, that is usually a few hundred euros per week, depending on their independent funding).

(I am willing to commit to travel and accommodation expenses from my own budget).

Try not to. Your institution is about to gain a very useful new knowledge, they should definitely pay for it. Also, you could probably get course credits, if you need them for your PhD.


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Do journals in general have any kind of policy regarding papers submitted by someone without a research affiliation?
Assuming that there are no ethical or legal concerns involved, in general, how would academic journals handle research submitted from the general public (e.g., if a carpenter were to perform a study on memory)? Would it be published if it held to the same standard as other research, or is it rejected without review?
Edit: A lot of people are commenting on the fact that a person outside of academia probably wouldn't be able to write in a way that was required or have the sufficient training for carrying out a proper experiment. Not my point. I just want to know if there is a general rejection of articles purely based on the fact that the person doesn't have any affiliation to a proper research organization. We could for example imagine a former Nobel prize winner who has a lot of money and prefers to work alone.

As far as I know, in just about every field it would be considered wrong to reject a paper merely because the author doesn't have a university affiliation.
However, as other answers have pointed out, a paper from a non-academic may have difficulty complying with the usual norms of the field for writing, and might be summarily rejected (or sent to a referee but quickly turned down after a cursory reading) on those ground.  Mathematics probably gets more amateur submissions than most fields, many of them downright crankery---although now that I think of it, it's been several months now since someone e-mailed me a one-page proof of Fermat's Last Theorem---and coping with them is a problem, in part because there is a culture that says formal journal submissions need an actual reason to be rejected, just in case this is really the one time a genius from outside academia has solved a problem.  But the converse is that as soon as such a paper does fail to comply with ordinary norms of writing and argument, there's grounds to reject it.
(By the way, your example is an interesting one because a study on memory presumably involves research on humans, or at least animals, which might have compliance issues---a carpenter has presumably not gone through the usual process of having research with human subjects checked by a board for ethical compliance, and I'm not sure journals would publish research which requires ethics review but didn't get it.)

I'm not sure to what extent journals ask/verify about human subjects approval. I've never been asked about it, and quickly perusing some of the journals in my field I didn't see any explicit mention of it in the author submission guidelines.

I left academia about 27 years ago after completing my doctorate and a couple of years of post-doc. Since then I have published about 6 papers on physics and mathematics in peer-reviewed journals so it is certainly possible to publish without any affiliation.
However, this week for the first time I experienced the rejection of a paper purely because of the lack of affiliation, so I can confirm that some journals are now rejecting manuscripts purely on this basis. The paper I submitted was arXiv:1401.8217 which reports my progress on Lebesgue's Universal Covering Problem including a new upper bound. This work is not going to make any seismic waves in the world of mathematics but it is a well known hundred year old problem and previous improvements on the upper bound have been published and well cited.
I submitted to the Hindawi journal "ISRN Geometry" because it is open access and currently has no article processing charge. These are useful conditions for someone with no funding or easy access to subscription journals. It was also convenient that they do not ask for TeX layout and will do the formatting to their style themselves. I had written in Word and was glad not to have to reformat.
After about two weeks I received a message from someone at the editorial office to say that I just had to submit a new manuscript including my academic affiliation for the review process to begin. I was given two days to do this. I replied quickly to say that I had no such affiliation. Two hours later I received a final rejection notice  "I regret to inform you that it was found unsuitable for publication in Geometry." No more details were given. The paper had not been sent to a reviewer and it was clear that the only reason for the rejection could be the lack of the requested affiliation. The person who signed the message does not have any academic record that I can find and is not one of the long list of editors for the journal.

I'm sorry to hear about your experiences.  I looked you up on MathSciNet and see that you're a serious mathematician.  It sounds like you deserve better.  It would be worth writing to the editor in chief and finding out officially whether your lack of institutional affiliation was the reason for the rejection.  If so this looks bad for the journal.  Finally, as a word of advice: you should submit your papers in (La)TeX.  It is freely available online, and anyone who can do mathematics can learn to use it.  Sadly, just doing this may help you get your work taken more seriously.

Pete, thanks for your vote of confidence. I have submitted papers in LaTeX before where required, but this journal specifically asked for submissions in PDF or Word. I do not understand why so many mathematicians consider use of TeX to be a useful way to separate out serious work. As you say, it is not hard to use and many works of pseudoscience are written with TeX while good research can be written with other systems. The journal has a list of over seventy editors but does not identify a chief.

You're welcome.  When I wrote "LaTeX", I really meant to typeset it using LaTeX and then submit the pdf file (that's what I always do; some journals will take the raw tex file, and most won't care).  As for the "I don't understand...": I'm not defending the practice, but just telling you something that I think might get your work published.  Concerning the journal: I had never heard of it before, but I looked it up just now.  Their description of "editorial workflow" is relevant and very nonstandard: see http://www.hindawi.com/isrn/geometry/workflow/.

Their mean turnaround time is 26 days; for a math paper that's somewhere between "impressive" and "suspicious".  Their practices prioritize fast results over results which are transparent or could be vetted for fairness in any way.  Although they have some distinguished editors, this is not an editorial model that I myself would be inclined to approve by submitting to.  I suggest you don't think too much of this and just submit to a different journal.

Almost every mathematician has a story about how she had to submit one of her better papers several times before it got accepted.  Most veteran mathematicians can tell the story with the best possible ending: the home that they eventually found for at least one of their papers was better than the journal to which they first submitted.  May it happen to you...

By the way: I would be willing to try to help you out more with this.  Please feel free to contact me.

Thanks for your help and advice. One thing to say is that since I am not career building I have no need for a respectable publication list so many of my papers do go unpublished. I do not want to support pay-walled journals and do not have funding for open access fees.

There are a couple of other geometry journals that would suit but they require TeX and I may also have to spend a lot of time reproducing the diagrams to a better quality. If an editor of a suitable journal were to invite me to submit (It has happened before) I would be willing to do that but I am not going to take the trouble if the paper is not guaranteed to even reach a reviewer.

I am now aiming to publish in Philica if they accept my membership. Originally they explicitly excluded independent researchers but "no" seems to have changed to "possibly"

This is really bad experience. However, I was working as a member of the Editorial board for one of the Hindawi journals and we had problems with massive amount of crappy submissions. Most of these were weeded out by non-academic editorial staff, but members of the EB received a letter where Hindawi asked us to be really strict in a review process. I guess they were concerned about SCI rating. (The journal has been since transferred to the different publisher). So in your case I assume that the explanation could be that they would resort to any means to cut the number of suspicious submissions

In general, it should not matter who you are, it is the quality and importance of the work you do that should determine the publishability. With that said, it is true that it is a nontrivial task to write with the appropriate tone, have the needed citations, and conduct a solid research effort without formal training. My advice to you, should you be considering publishing in a technical area (if you are the carpenter in question), would be to find someone who works/publishes in the area with the aim of writing something together. Chances are they may have some good ideas on how to structure and present the work, how to formulate the basic hypotheses and ideas so that they will be palatable to the journal.

In principle, there's nothing stopping a paper from being published by a private individual. However, in many fields, the bar to realizing a publishable "quantum" of work is so large in terms of equipment or other resources required that there's virtually no chance of anyone without exceptional means could afford it.
That said, there's also nothing that requires a journal to accept a paper from a private individual, either. Journals regularly return papers without review; one criterion for accepting a paper could very easily be that the authors have affiliations witbh "verifiable" organizations.
However, once a paper has been forwarded for review, it should absolutely be reviewed on an equal basis to any other paper in the journal.

When it comes to many experiments in cognitive psychology (where you basically only use a computer monitor to present stimuli on), I would say that the equipment I own is better suited than what my department have. That is, I have a fast computer, with a big, high-resolution screen (not a CTR that is), and I have comfortable chairs (in comparison to old, squeaky chairs).

@Speldosa: That may be true—but I'm thinking more of sciences and engineering, where the analytical equipment can run into the tens or hundreds of thousands of dollars for cutting-edge devices.

In the Humanities and Social Sciences there are no formal restrictions against submissions by members of the general public.  Some journals are far more friendly to non-academic researchers, either due to editorial staff or a culture of supporting popular contributions to knowledge.  (History from below and socialist research programmes in general have an openness to knowledge from outside the traditional academy).
The largest barriers to entry are of course the methods, language, evidence and "currency of research" required to conduct and produce research to scholarly standards.

If you want to appear in a motorsport magazine as a racing driver, you will need to belong to an approved team and comply with all the rules of the activity. If any requirement is missing, even if it is minimal, you will be left out.
Motorsport sponsors protect their interests and impose conditions. They can pay a lot for technical optimization and can pay pilots to spend all their time intensely training. So do the sponsors of science.
Do you listen to fans of motorsport complain about the imposition of conditions in the activity? Obviously there are no such complaints. Why then, who are out of scientific sponsorship, want to complain?

As it stands, I don't think this really answers the question. I think I can see where you're going with your analogue, but it seems to somewhat unrelated to the actual question.


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Advantages and disadvantages of doing PhD research at a non-academic lab
What are the advantages and disadvantages of doing your PhD research (in science, math, or engineering) at a non-academic lab (like a government or industrial lab) vs. the traditional academic setting? (Of course, the degree is granted by a university.)
When is one option better than the other if you have the choice between doing your research in an academic or non-academic setting?
A few potential advantages I can think of:

You're likely to be hired by the lab after graduation. If you don't want to enter academia and are happy with the lab, this could be your career. If you do want to enter academia, often you're in good company because leaving research labs for academia isn't uncommon.
You can work with more people (your school's students and professors and the lab's researchers). This'll expand your professional network and expose you to different perspectives.
Your affiliation with the lab could add some credibility to you and your research.

A few potential disadvantages:

Travel could be problematic if your school and your lab aren't close. This could be mitigated by taking care of the coursework first.
The research topic is often dictated by someone in the lab if you are funded by them. If you decide this topic is not worth researching or not interesting then you might have a problem. Politics in the lab could change the research topic in the future and that might also be a problem.

Throughout graduate school I worked at and was funded by a university-run laboratory that operated somewhat like a government laboratory and was largely funded for applied research. I now work at a UARC (which is similar to an FFRDC).  Given that my graduate school lab was already affiliated with the University, though, my situation is slightly different than yours.
At least in the US, it is relatively hard for non-academic laboratories to find funding for basic research; funding agencies like the NSF have a prejudice toward funding degree-granting institutions.  Therefore, in my experience, much of the flavor of the funding at non-academic laboratories is geared toward applied research.  This might not be a problem, but it can be a challenge to find a deep, Ph.D.-level problem to solve when your sponsors are interested in seeing more concrete results.
In my case, working at an applied research laboratory to fund my graduate degrees was actually somewhat of a benefit.  Due to the reasons I listed above, it was difficult for me to latch onto a deep problem to solve for which there was stable, direct funding.  Therefore, I used my position at the laboratory to basically "pay the bills" (it covered my stipend, tuition remission, &c.).  That gave me the freedom to work on related—but not directly funded—problems that interested me.  This of course had the overhead of essentially working two jobs at once, but it had the added benefit of providing visibility to my "side" research to the sponsors who were funding my "pay the bills" research.  It also paid for my trips to relevant conferences, at which I was able to present both flavors of my research.
Now that I am working at a UARC, I see others here who are also pursuing part-time Ph.D.s.  Most of them seem to have found a similar model to mine: They use their position at the non-academic lab to "pay the bills", and then focus their actual research on a related but independent problem.  If you are able to fund yourself (i.e., if your Ph.D. advisor doesn't have to worry about finding funding for you), then many advisors will be willing to take you on as a student.

I could see that a lab might want more applied research whereas a PhD might be more theoretical. Good point. Someone who does more theoretical work would have a little extra work to do. Thankfully in my case the proposed research topic is a mix of theory and application, and I'm interested in both.

Since a Ph.D is always granted through some kind of Ph.D granting institution (usually a university) I assume your question is about being funded by a research laboratory while being formally affiliated with a university ?
As with most things, it depends on the context. First of all, I wouldn't be so sure that a permanent job is guaranteed. Unless you have an explicit letter in writing saying so, nothing is set in stone. Secondly, I'd worry about your potential future marketability in the event that you do have to look for a job elsewhere. Again, whether this is an issue depends on the specific context of your arrangement. Finally, your last "pro" about working with students AND researchers may not be true unless the lab and university are relatively close to each other. There's also the risk of your advisor tuning you out, unless there's already a structure of collaboration in place.

I've clarified the original question. Some PhD students are funded by a lab (as I would be if I took an offer I'm considering). Others merely do research there for any number of reasons.
As for the job part, I did say likely because I'm not so sure. But the few folks I know who went this route did get jobs. In fact, some programs that promote this sort of collaboration require the PhD student to take a job at their collaborating lab for X years.
Do you have any other thoughts? I'm aware that my list items have exceptions.

Overall, it's fine as long as you're able to do research, and don't end up just being a programmer or something like that. You should have the freedom to publish, attend conferences, and do all the other academic things that your university colleagues can do.

I am currently doing basically this in the UK. I can definitely say it is a viable option, although there are definitely some drawbacks.
The biggest disadvantage is that you lack lots of the support the being based at a academic institution has. There is no student union or similar structures to support you. While you will have access to these facilities via your academic institution they are generally much harder to access due to your physical separation.
Similarly the social life at non-academic institutions is very different. Most of your colleges will not be students and probably have a very different outlook on life, e.g. many more older people with families. Similarly there is no union, clubs or other formalised ways to meet people socially. Although this probably depends more your personality and the specific place your at.
You are also correct that travel to/from your academic institution can be very annoying. For meeting with your supervisor I strongly recommend trying to do as much by skype as possible.
Finally non-academic institutions, even government labs/NMIs tend to be less research focused and more focused on providing a service/developing a product, which might involve significant research. This isn't necessarily a problem as long as your project is well defined and your not at risk of doing several small unrelated projects.
On the plus side, you will probably be more exposed to industry and get a wider understanding of what is viewed as important by end users.
Many of the researchers at these labs are world-leading in there own right and some labs are very highly regarded which can't hurt your future prospects.
Also, they are presumably providing funding for the project. Which is always import to have :).


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Will getting a PhD close doors for working as a software developer?
I am trying to decide whether I should continue with a PhD (in a field closely related to computer science) after my MS. I will be finishing my MS soon and have an opportunity to continue for a PhD.
My question is will getting a PhD close doors for working as a software developer? Are the opportunities for PhDs' only based on research? Even after a PhD will I still be able to compete with people with BSs and MSs for Software Engineering positions? Finally, during the PhD will I be able to apply for internships that deal with software development than pure research?

Q: Will getting a PhD close doors for working as a software developer?
A: It depends on the position you are looking for.  Certain employers will not want to hire you because they may have the perception that hiring someone with a PhD will be more expensive than hiring someone with a bachelor's, and if someone with a bachelor's can do the job, they aren't going to want to pay extra for the PhD training.
Q: Are the opportunities for PhDs' only based on research?
A: No, there are a number of PhD graduates who go into industry and end up doing development-focused work.
Q: Even after a PhD will I still be able to compete with people with BSs and MSs for Software Engineering positions?
A: Yes and no.  If the job can be done by someone with a BS or an MS, then companies will not want to pay more to get a PhD to do the job.  On the other hand, there are development-focused positions where a PhD is beneficial.  Having a PhD opens those doors for you.  Some of this will be very dependent on what you spent your PhD doing.  For example, if you spent your PhD developing systems and publishing papers on those systems, that will be much more desirable for companies with software development positions than if you spent time doing non-implementation research.  At some software development companies, having a PhD is considered equal to some amount of experience, so you may enter at a higher position/pay scale than someone with a BS or MS and potentially get promoted more quickly.
Q: Finally, during the PhD will I be able to apply for internships that deal with software development than pure research?
A: Absolutely.  This will be somewhat subject to your advisor, but there are a number of internships for CS graduate students that are very development-centric.
There are a lot of different reasons for getting a PhD, for example, your own personal gratification, to do research, to teach, to get a job that you can't get without a PhD.  The question I think you should ask yourself is, "What do I want to get out of doing a PhD?"
If the answer to that is to make more money/make a bunch of money doing software development, you should stop at your MS and go into industry.  If you are doing it for other reasons (as listed above) then definitely go for it.

Regarding the first question, for some jobs and employers, having a PhD has the cost of opportunity of not having industry experience. Some employers don't even count a PhD as experience (but you probably don't want to work with them).


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How should I format code words in my personal statement?
I'm applying to Master's programs for Statistics. In my personal statement, I mention the names of some R packages like car, ggvis, and effects when I talk about professors that I would be interested in working with and some of my own research. Typically when people write about these, they are just all lowercase letters, not italicized or anything.
It looks really weird in a regular Word document, especially since "car" and "effects" are regular words. I'm afraid that it may look out of place. Is it okay if I change the font to the code font so it looks like ggvis and effects? I wouldn't use the grey background, but the serif typewriter font is pretty standard for bits of code, right? I'm afraid it will look unprofessional for academic/business writing.

You can use some typewriter font for those.

Probably you are thinking about this too hard: as long as it's clear what you're saying and choosing a reasonable form of presentation, it's probably fine.  Monospace font is one way to do this, another way is to put the names in quotes, just like you did in your question.
If you want to be really cautious, you can look at scientific papers from the field and see what conventions people tend to use.  That way, you will be certain that your readers will find your presentation familiar.

I'd pick a monospace font, yeah. For extra style points, use the same monospace font for your email address and any URLs in your CV.

I'd pick a monospace font — I wouldn't. — For extra style points, use the same monospace font for your email address and any URLs in your CV — No, please don't!!

@JeffE - Clearly you feel strongly about this.  If you share your reason(s), maybe you'll convince me!  Also, could you propose an alternative for the OP?

I would recommend following the style guide in the official R documentation, which is to typeset the package name with a bold font.
See this related question. The answer I'm posting here is given on that page in a comment on the original question by Massimo Ortolano.

Can you point to where exactly the documentation says that?  I don't see it, but I do see that the document does not typeset package names with a bold font.

@Edward you are right. I may have misinterpreted the comment as saying there is some explicit statement that the names should be bold. I can't find it either. But I do see the package names are set in a bold font at least in the short introduction to R html document.


text:
Permanent document identifier requirement for DBLP indexing?
First of all we are holding a conference which is the 12th year of this conference. All english papers of this conference from the 7th year are indexed in IEEE, however for the first 6 years there exist no document identifier over internet. We would like to index this year's conference papers in DBLP in addition to IEEE. I have read this page about the requirements to index proceedings of conferences in DBLP.
So there are my questions:

Since there are no permanent identifers for the first 6 years of this conference is it possible to index papers from the 7th year up to now in DBLP or it should be a complete collection of all 12 years of conference?
In the DBLP help page, it's noted that

All contributions should be registered for permanent document
  identifiers, such as DOI.

May an Arxiv identifier be accepted as a permanent document identifier for indexing in DBLP?
Any answer would be appreciated.
Thanks in advance.

Your best bet is to ask the DBLP administrators directly; they are remarkably responsive, in my experience.  (DBLP does index arXiv preprints.)

JeffE is correct, you should contact dblp@dagstuhl.de and state your case. As a general guideline, DOI is a best-practice example of a persistent identifier. In fact, more that 80% of the documents in dblp do carry a DOI, including even many historic papers. There are other handle systems or even just well-structured URL schemes of digital libraries that are accepted by dblp as well, but assigning DOIs is currently the way to go if you want your publications to be found in years from now.

@MRA Can you please turn your comment into an answer, so that I can vote for it?

There is no reason that DOIs cannot be issued to past issues of the conference proceedings. They will have to be re-indexed of course, so that they can pick up the change in metadata.


text:
How to improve chances of admission to Ph.D. program for international student?
Question synopsis:

I have a postgrad degree, a couple failed classes on transcript but
  did well in others; tried applying to PhD programs in different
  countries, but did not get accepted and had poor luck hearing back
  from professors, nobody seems to care. What to do?

Note: There was a question similar to the one below that was deleted as I was finishing writing the answer. So the answer did not get posted but I was able to save it. I figured it might be helpful to keep it in the system in case it might help someone in a similar situation. Below is my take.

Here are some basics that can play a role and improve one's chances, from a U.S.-centric point of view:
Some assumptions:

Your postgraduate degree is reasonably recent (preferably immediate prior year or close, with relevant experience in between). If there was a lengthy break with seemingly unrelated work in between based on what you want to study now, this complicates things.
You are applying in the same general discipline as your postgrad degree (e.g. Marketing, Mechanical Engineering, Psychology).
You had good letters of recommendation. If they had any flags that might give cause for concern for admitting department, that is a problem that you need to iron out prior to sending out any more applications. If you have reason to think this may be the case, it may be best to approach your recommending faculty honestly about this and see if they can either share a copy of the letters they wrote for you, or tell you if they mentioned anything that might explain slow uptake.

Communication with faculty:
- evidence of "passable" English proficiency (if non-native), or (if native) ability to write in pretty much perfect English with no grammer or, punctuation errors.
Admission materials:
- Have all your applications been "cold," i.e. with no personal connection to / past interfacing with the faculty whom you contacted? In other words, have the letters of recommendation (which I am assuming
If so, this might explain reticence to respond. The Academe is a fairly tight community of several thousands or hundreds of individuals in any given narrow field. The "first order" professional networks tend to be on the order of a couple dozen past/present collaborators. Faculty tend to be more comfortable receiving a recommendation from someone they know rather than a complete stranger. So ask your professors who write your recommendation letters for contacts they would recommend, and tackle those programs as priority #1, gradually widening to "outer rings" of your recommenders' professional networks.

Maximally polished, edited, proof-read, 100% perfect letter of interest (cover letter/whatever they call it). The letter must show evidence that you have done your homework and are aware of the latest research projects of the faculty whose work most closely fits your experience and interests and who you would like to advise you.
High score on GRE or other applicable standardized graduate entrance exam.

Funding source:
 - As has been suggested elsewhere on this forum, I would avoid stating anything about the fact that you are not seeking funding. This self-qualification might come across as, "I am hoping the fact that I am a cheap date will sweeten the deal." This might work in some odd cases, but most reputable, large research universities tend to be more concerned with attracting high-quality applicants rather than affordable applicants.
If the department considers the applicant to have potential and leans toward admission, but there is no funding, they will communicate this though an admission decision without corresponding offer of Research or Teaching Assistantship. This leaves the ball in the applicant's court, and things work out through natural attrition. (For instance, I had no offer of support first year, so found a Research Assistantship with another research center on campus that was closely related to my field, and it ended up a good fit.)
Networking:
- Have you met, or at least read / cited in your thesis or research papers the professors you are contacting? Professors like applicants who do not only talk the talk (in a cover letter) but walk the walk, having used their theories and cited them accordingly in written work. Naturally these pieces also make for good writing samples, if the department and/or the Graduate School requests those as part of the application.
Finally, basic psychology suggests that applicants who behave like pests which, if not kept at an arm's length, would swallow all of a professor's free time and clutter his/her inbox, are less attractive, than applicants who communicate no more than necessary as part of the application process, and follow-up only with good cause and after first trying to get answers with the Graduate School and/or department's admissions office. Professors value their time immensely, and aggressively prioritize what emails they respond and do not respond to. They are not trying to be rude, it's just a professional adaptation to an environment with multiple competing priorities and limited time. So you want to come across as someone who recognizes this and helps them spend less, not more time addressing your inquiries.
UNLIKE THIS EMAIL, if you do email faculty, keep your email inquiries SHORT: 3-4 sentences, and get to the point in the first or second sentence. Begin with a question and request, and end with context. Professors often do not read to the bottom of every message.
Communicating through the appropriate administrative channels and only when necessary beyond the formal application process makes you appear confident, and confidence may be perceived as evidence of having other options. In a sense, you want to balance being courteous, excited, and a little reserved at the same time.
Finally, I would encourage to consider looking closer to home. Why apply to all continents if there might be a great program a few hours away in a neighboring town in the same country...but I recognize there may be other factors at play there.
I am sure I am missing some other important details, so extensions/comments welcome as always.

I +1'd, but this answer mainly applies to graduate students in general. 10% of the answer is about having good English, which of course would be necessary if applying to an English-speaking institution, but what about the reverse? My top school of choice is in Japan; language skills are generally an implicit requirement... That said, what about passport/work visa, etc? Surely you can't just live in the U.S. for a few years with no documents.

Good points. I figured the question is related to English since OP mentioned applying to different "continents," and English tends to be the common denominator in this regard, although it could be French or Spanish in certain cases. (Also, living in the U.S. carries the risk of assuming that America is the only country in the world, and English the only relevant language...впрочем не обязательно ;) Did not address visa issues as question focused on acceptance to a PhD program, rather than gaining entry into the country post-admission, since that's a non-issue prior to  acceptance...

True, English tends to be the common denominator in academic settings, especially in English-speaking countries (of course), though there definitely are other languages spoken. I mentioned the U.S. because that's where I live and the only country  (aside from France) whose visa laws I am familiar with. Are there other factors for international students specifically? If all goes according to (my) plan, I'll be studying in Japan, so this question is very interesting to me :)

As someone doing a PhD in the UK, the admission details in this answer seem specific to how things work in the US. We don't have letters of recommendation here - we just provide details of a couple of people willing to write a reference for us. These would only get requested if you were considered as a candidate based on the application. I agree with the advice regarding communication with faculty. Nothing worse than receiving an email that is an obvious cut and paste from one sent to another professor!