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Number of citations after PhD
I am trying to compare PhD training programs of different universities, institutes and departments in my field of interest. One of the comparisons I made is where did the previous students go after they finished their PhDs; how many papers did they write during their PhDs; and how much are they cited 1-2 years after completing their PhDs.
Now, comparing the citations counts is difficult. They vary quite a bit. How many times should  a successful young scientist be cited 1-2 years after completing his or her PhD? How about an average one? What is the minimum number to be able to continue in academia? I understand that exact numbers are difficult to provide but I would guess you senior scientists can provide good estimates.

Such a short time after publication the number of citations will mostly represent how well a paper was advertised rather that its quality.

Try and check sucessful scientists: In some fields (math/TCS), only like 10-20% of their articles really get significantly cited, most have up to ~5 citations. If you really want to evaluate their publication quality, look for eaxmple at cooperation scheme: Do they publish only student+supervisor? Do they publish in larger teams across the dept/from other departments/universities/countries? If they do, look at the profiles of their coauthors: Good scientists wouldn't publish with students from bad departments.

I believe that scientometric indicators of scientific productivity and impact are at best, limited if the overall objective is to compare different college, departments, universities, institutes, centers (or any other academic organization) in one discipline. This is coming from someone who has had rigorous training in bibliometrics/informetrics/scientometrics.
This is because there are massive variations in citation patterns within a particular field. This is especially pertinent if the field is rather interdisciplinary. Note though that in any given field, there is a general level of agreement among scholars in that field which departments are "better" than some other ones.
For instance, in Human-Computer Interaction (HCI), critical theorists and ethnographers get, on an average lower numbers of citations per article published than say, ubiquitous computing folks.
However, purely on an exploratory basis, there could be several ways of looking at departments:

Where are graduate students from a particular department publishing in?
Are they consistently publishing in top tier venues? e.g. In core HCI, I would look at CHI/CSCW conferences. When considering, the subfield of usable privacy, I would, in addition, look at SOUPS/IEEE Privacy & Security.
Among these publications, are they receiving best paper awards or best paper nominations?
Where are students from these departments being placed on a consistent basis? Are they being placed in industry or academia? Where, specifically? Google or a no-name startup? Are they getting tenure track positions or primarily post doctoral fellowships? Which other departments?
Are some of these students recipients of prestigious fellowships during their doctoral studies? e.g. NSF Graduate Research Fellowship or Facebook Fellowship? How many?
Bibliometric Indicators:

Average number of peer reviewed articles? (full journal and conference papers)
Average number of citations per article?
Co-authorship network analysis (which gives a nice idea of collaboration networks)
Average number of student grants received or otherwise?

You can go on and on and on.
The idea is that, there is always some way to standardize or normalize any given construct. Sometimes, that is an useful approach. But, strict adherence to bibliometric indicators at many times, make you mistake the noise for the actual signal.
Consider the bigger picture and use metrics to buttress your concerns. That might be a more holistic approach.

Although this approach to measuring is plausible, I fear it is not what you want. Although of course things vary by field, the papercount per se, or even "impact factor", or ... any other easily-measurable thing is not quite what will affect things.
At least in mathematics (my field), a smaller number of very-good papers is much better than a large number of irrelevant papers. One might imagine that this would be measured by "impact factor", but it is absolutely not reliably so. As an extreme case, consider what happens when an important problem is finally and definitively solved: there may be fewer follow-ups, fewer citations, simply because there's little more to say.
And there's time-lag: I have many examples of 10-20 year (and longer) delays before people widely realized the interest of a given paper. Srsly, surely we're not trying so much to be of-the-moment-celebrities, but to make a long-term impact.
One could go on-and-on about the unreliability of appealing-but-fatally-flawed metrics... but the real point is that a less objectifiable judgement is necessary to evaluate the "merits" of a program. Stats on the students is probably not quite what you'd want, even though it might seem to be. E.g., at more elite places, there is vastly greater variance among students... so the "outcomes" are harder to interpret meaningfully... and, for you yourself, what those other kids did or didn't do is operationally irrelevant:
That is, your level-of-performance, that causes (or doesn't) respected experts to commend you to their peers, is what will get you a job, or not. The "published papers" thing is a side-effect.

This was a good answer too!

You should decide on your PhD institution by the quality of the tenured faculty, not their students. Great students make great co-workers, but it's the quality of your supervisor that can make (or break!) you. If you have good relationships with faculty at your current institution, you should ask them what, in their opinion, are the best departments to apply to.
You should review the publications of faculty members you would like to be supervised by, to see if their research interests you. The papers that are first-authored by the faculty member (they are still active in research and don't spend all their time supervising and teaching, right?) will be particularly useful in this regard.

In most fields, the faculty in all of the top 200 schools would be coming from the top 20-30 programs, and thus will all be highly qualified to teach and supervise. However, it is the quality of the student body, and the peer effects associated with it, that make programs superior. MIT can afford to select the best of the creme; UMass Boston will have to do with the grad applicant leftovers that were not placed to better places. And the faculty, that may only be a notch worse at the latter, would have to offer simplified courses because their students won't be able to digest the "real" ones.

@StasK - in that case, surely the best universities would be able to select the best faculty, as well as the best students? Think carefully about why the university continues to be at the top - great faculty. Of course, excellent researchers are not only found in the top-20 universities, which is why I try to emphasize the importance of your supervisor while making my answer independent of country and discipline. Not all PhD programs have a significant coursework component.

I disagree. The success of past graduates of a program is a far better indicator of the likely success of future graduates than the success of current faculty.  Lots of incredibly strong, active, funding-rich faculty are terrible advisors.

@JeffE I concur.  However, the value of PhD advisor goes beyond teaching purposes.  If one intends to pursue an academic position, a top research group would likely be a better choice even if that scientist is not a perfect advisor.  By being in a successful research group, a student can work at the very frontier of the field and can potentially make a great impact; a successful scientist often have significant influence in the field and many academic connections.  These alone don't make their students good scientists, but certainly can be great boost to the career of new scientists.

I the disagreements might come from looking at the problem from two different standpoints - as a whole, then overall student performance is a good point of judgement. But my answer takes a more individual standpoint. Excellent funding and publications mean little if the supervisor is a poor advisor.

I believe your first two criteria are far more relevant than the third one. Two years after the defence is too early to evaluate scientists based on citations. Moreover, the average number of citations varies a lot from one field (or even subfield) to another.


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Moving a detailed literature survey in Appendix to reduce size of chapter?
In my dissertation, I am solving a problem by using techniques used to solve another problem. As a result, I have to do two literature surveys for both problems. I ended up with a huge chapter!  - most of it is basically a literature survey.
I do not want my examiners to hate me when they find a long thesis, but I don't want to get comments such as: "Why have you not considered the work of X in your survey?"
Is it a good practice to move part of this huge chapter's survey to an Appendix chapter, while keeping a section that speaks about the general approaches followed in the literature?

For a thesis, you may as well include the full review. You've done the work, and a thesis typically has no particular length limit. Realistically, your examiners will probably just skim it anyway. I see no reason to move it to an appendix, though I also don't think it matters very much. If your advisor or university policies feel strongly, of course, do what they say.
When you publish papers based on your thesis, then you'll want to condense the review to focus on  the most important and relevant prior work.

Disclaimer: I am a current graduate student starting to write my own doctoral dissertation.
The advice which I have got from several faculty members with whom I have been working for the last 3-4 years is that there is no true length to a literature review.
A literature survey should encapsulate your research problem, identify the current gap in the literature and then, factor in methods using which you attempt to answer your research question.
If that makes it long, its long. My literature review is probably around ~30-40 pages. Given that I work in a rather interdisciplinary area, its inevitable.
I advise you to include all the literature that is relevant.
The appendix is usually reserved for additional figures, tables, links, code, supplementary analysis etc.

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Should I ask permission of my co-authors when republishing an article?
In the university that I am working, which is more technically than research oriented, they want me to publish one of my past articles in a faculty magazine that they are planning to print. I have chosen one from the IEEE, and I have read that they have that possibility. I would like to know if I should mention that to my other co-authors or is it not necessary?
Thanks for your help

Yes.
As a courtesy, one should always inform co-authors of such things. One doesn't necessarily expect replies (since no action is required...), but one is taking action on "property" that is partially "owned" by other people, so some notification, or even request for permission (which would presumably be unhesitatingly granted), is entirely reasonable.

in other words, if "your" paper has co-authors, it's not really "yours" :)

I thoroughly agree, and this issue can arise even with a single author.  One of my papers was reprinted in a book without anyone telling me.  (The publisher gave the book's editors legal permission to reprint it, and I guess the publisher thought the editors had already discussed it with me, while the editors assumed the publisher would notify me.)  This didn't cause much harm, but it did embarrass me a little: the first time anyone asked me about the book, I confidently explained that they must be thinking of someone else's paper.

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Intellectual Property Assignment Agreements for Ph.D. students - What is normal?
As an incoming Ph.D. student I was asked to sign an intellectual property assignment agreement in addition to an employment contract as a condition for receiving a tuition reduction and a stipend.  The wording was rather vague, and contained 'legalese'. I have no experience with this. So, I do not know anything about it, and I do not know if the "agreement" I signed contains anything abnormal, because of the way it was written.
Is this normal practice?
If so, what is contained in a standard intellectual property agreement?

Google started as a project of two Stanford grad students, and Stanford got a share of the stock. Presumably this is the purpose of this agreement -- in case you start the next Google.

Most universities make their policies public (sometimes as part of a student or employee handbook), including IP policies, so with a little research you can probably find the policies of a variety of universities, and get a sense of what is standard.

It's a bit hard to answer your question, since your description of "rather vague obligations" is, sorry, rather vague. That said, this sounds like the kind of IP assignment you will need to sign when you start any kind of job, too. Neither companies nor universities are keen on your inventing something cool on their dime, without them getting a part of the action.

That "to assist in perfecting and protecting its rights to such property" is most likely innocuous (no legal advise here!), as it (most likely) merely requires that you not passively obstruct the university's getting its share of stuff you produce on its dime.

@paulgarrett: That's probably the main thing.  But I would guess that, for instance, if you invent something at the university, and they patent it (maybe jointly with you), and then years later someone challenges the patent, they might invoke this part of the contract to get you to come and testify about the work you did on it.  I'm not a lawyer, etc, #include <stddisclaimer.h>

(@NateEldredge, good combo hashtab-semblance + C-lang include-file syntax! I'd not realized the coincidence 'till now. And, yes, your observation...)

Don't sign anything you don't understand. It is important that you understand the written contract to make sure that none of your rights are being violated. If it is really difficult to understand, I suggest that you ask a lawyer on the terms of the agreement and on what is the best way to respond to such agreement.

Very roughly, at the US universities I have worked for, the IP policies have been along these general lines:

When you write a paper or book as part of your research, you get to keep the copyright and any royalties.  But the university gets permission to use the work internally, keep a copy in the library, etc.
If, as part of your research, you invent something that's patentable, contact the university's IP office.  They will help you with the patent process.  You and the university will hold the patent together, or some similar arrangement. They have to agree on any licensing agreements, etc (where you sell some company the rights to use your patent), and they get a large share (perhaps half or so) of whatever royalties or fees are earned.

(I'm a pure mathematician, and we never invent anything patentable, so I always skim the patent part and may have got it wrong :-)

RSA was invented by 3 pure mathematicians, right?

@Oxinabox: The distinctions are not always clear, but Rivest, Shamir and Adleman all have PhDs in computer science rather than mathematics.  While I'm sure pure mathematicians would be honored to count them among our ranks, I don't know that they would see themselves that way.  Also, although the RSA algorithm was patented in the US, there was a lot of controversy as to whether the patent was properly granted, and in fact it apparently was not able to be patented elsewhere.  If the patent had not expired when it did, it might well have been challenged.

(But despite my serious defense above, that remark was mainly meant as a joke - hence the smiley.)

Rivest, Shamir and Adleman all have PhDs in computer science — Specifically, in theoretical computer science. So yes, they are (or at least were) pure mathematicians.

Thanks for the extra in formation. I am pleased to become more educated.

+1, but I'd say if you invent something that's patentable, try to publish it under a free license as soon as possible before the university gets a chance to patent it. That way nobody can restrict public access to knowledge in order to make a buck.

@einpoklum: I'd hesitate to give that advice without knowing what the university's policy says.  It may very well say that  you're required to inform the university of any potentially valuable invention, and give them a chance to patent it, before you publish it.  If you release something that turns out to be highly valuable, you could potentially get fired and/or sued.


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Should I use lighter or heavier paper for my printed dissertation?
My university requires one to submit a printed copy of the dissertation. The paper has to be 100% cotton, white, and 20- to 24 lb weight.
Since I have a choice in the weight of the paper, my question is if there are any advantages to one weight over the other.

Go to the print shop. And ask to see if you can see/feel samples of different weight paper. (Better yet, see/feel documents printed on different weight paper.) I would say that the difference is certainly noticeable, but it is up to you whether the difference is important.

Lighter paper is usually slightly cheaper. And your finished book would be also lighter (pretty much by definition); this may or may not make a difference for when you carry it to the various offices/libraries as part of the process of finishing your degree.
Heavier paper has a better "feel" when you flip pages (think about the difference between a high quality hardcover book versus a cheap paper-back novel). It is a bit more resistant to wear and tear, and if you scan/photocopy pages it will be less likely to have the effect where the "next" page shows through.

If the only publicly available copy of your dissertation would be the copy you submit, I would ask you to do would-be readers a favor and use heavier paper. But if you intend to publish your thesis (take chapters and publish them as journal articles, or just put the entire thesis online for the world to see), then the lighter paper will save you a little money, and perhaps be marginally better on the environment.

I don't think the weight of the paper is as important as the material from which it is made. So long as the paper is "archival quality," meaning no acids or other components which will allow it to degrade more easily over time, the choice is somewhat arbitrary. Willie Wong raises some valid points in his answer, though—the slightly thicker paper will help future readers more than the thinner paper, and the relative change in weight is probably not so large as to make the thesis cumbersome as a printed volume.

This is exactly what I decided to get...until I tried to find A4 paper in the US. The three options available didn't include "archival quality". Still, +1 for the info.


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Private Git repositories for students, that don't become public later
Note: This question was asked before GitHub offered free private repositories.
Short version of my question: Is there a good way to provide students with free, private, Github-like git repositories, that won't become public later?
Background: In computer science, it is considered best practice to use Git (a version control repository) for software development.  Many universities want to encourage students to follow those best practices as part of their coursework, so they'd like to encourage students to do the same.  However, they don't want student work to be made public, as this creates a temptation for cheating.
Github in particular is popular, as it provides both Git repositories, an easy-to-use web front-end to Git, and a convenient workflow for collaborating using Git.  Github is free if you make your repository public; normally, you have to pay for a private repository.  Github has a special program for students: as long as you are a student, you can have private repositories for free, if you sign up for their student discount.  However, this only lasts as long as you are a student.  After two years, the student discount expires, and then the private repositories are locked; if the ex-student wants to retain access to their repositories, the ex-student has 30 days to either pay Github a monthly fee to keep it private, or they can tell Github to make it public and pay nothing.
One university I'm familiar with encourages CS students to sign up for a student Github account and put their projects and homeworks in private repositories.  However, empirically, Github's policies seem to encourage a certain number of students to make all their repos public after they graduate and their student status expires -- and then solutions are available on the Internet.  Because good software development projects are so labor-intensive to construct, many courses re-use projects for several years in a row.  Current students have reported finding this by search and are a bit worried that it'd be so easy for other students to cheat.  Therefore, recommending that students use a private Github account seems to create a two-year time bomb that will have unfortunate consequences for courses who plan to use their project for more than two years running.
Is there any good solution to this?  Is there a better alternative than Github that can be recommended to students?
In particular, a better alternative should meet the following requirements: allow students to have Git repositories for software development and collaboration with project partners; is free; is private; will remain private over time, without encouraging/requiring alumni to make their solutions public if they want to retain access to their solutions without paying; doesn't create extra work for instructors to constantly search Github to look for inadvertently-public solutions from past semesters.
I've seen How to deal with student putting their (home)work on github, but the solutions there aren't workable in this context: creating new projects every semester is not a good solution (it's been tried and leads to pedagogically inferior results).

What about running your own GitHub server: http://stackoverflow.com/questions/8390828/how-can-i-have-github-on-my-own-server ?

I suspect, if you are reusing project, students are more likely to get old solutions from their friends who took the unit last year, than by finding a random solution on github. Therefore, this is a nonissue. Why worry about locking the dog door, when the window is wide open?

@Oxinabox, empirically, we have had cases where people find a random solution on Github (sometimes not even trying to cheat; occasionally deliberately cheating).  So while what you're are saying makes a lot of sense... practice doesn't quite seem to bear that out.  We have empirical evidence that it isn't a nonissue.

I don't understand what would prevent a student from putting publicly online their projects after they graduated, even if the repositories remain private.

@MassimoOrtolano, obviously, nothing prevents it, except possibly for fond memories of their alma mater and desire for other students to have a chance at the same experience they had.  My experience is that ex-students aren't generally going to go publish solutions to past projects after the fact... unless their hosting service provider (e.g., Github) forces them to do so for some reason or another.

For my private repositories, I'm using gitlab...

Update January 2019: GitHub now has free private repositories.

Bitbucket offers unlimited private repositories. I use it for this purpose.
You can also host your students' repositories yourself on your own server with Gitlab (the community edition is free). This option has the advantage that you aren't asking your students to trust a third party with their data. I sometimes use this option, too. It's very easy to set up.
However, having students' work in repositories that don't automatically becomes public doesn't obviate the need to create new projects - students can still opt to post their work publicly. (This is true even if you don't use Git in the course at all.)
Personally, I typically use Bitbucket and ask students to keep their repositories private for the duration of the course (so as not to make cheating too easy), but they are free to make them public later. Part of the appeal of project-intensive courses to students is that they create something they can show off to potential employers. I want my students to have the option to make their work (which is often very impressive, and which they have put a great deal of effort into) public, so that they can enjoy this benefit.  I occasionally see students publish their repositories, put a link on their résumés or LinkedIn profiles, and then continue to improve their projects for months after the course is over, which is extremely gratifying.
I would consider it a disservice to students to prevent them from showing off their work after the course is over or after they graduate, even if I could prevent this. My university does not claim ownership of intellectual property produced by students in the context of uncompensated coursework (unless there is an explicit written agreement stating otherwise), so unless their projects also include material which I hold the copyright to, I couldn't stop them from publishing their work even if I wanted to.

IIRC, bitbucket's free private repos are only for academic users - so I'm not sure what happens when the student's university email address stops working. But agree with the rest of this answer.

@Simon nope. free private repos for any individuals and teams of five or less. (With academic account, you can get > 5.)

Ah, right! I stand corrected :-)

There are two other variations you can use with GitHub that are related but independent of the free "Student Pack" features.
Both of these options are free for instructors and are generally preferable to just telling students to get the Student Pack and set their repositories to private.
Either one may work for your needs, but both have some quirks and tradeoffs currently. There are so many subtle details I can't list them all here, plus they are actively developing and changing things. But here's a summary of my experiences:

"GitHub Classroom".  Last year I tried this option for several assignments one semester.  It might work for you, but ultimately I got fed up with the assignments workflow and the fussy "Rosters" it uses. It also prevents students from using the "Fork" feature at all, nor much of any of the other repository admin features. Instead of fork, it has a goofy and error-prone replication feature when they check out an assignment. Another design flaw is that anyone who manages to get the assignment link will be granted access to a copy of the assignment, regardless of whether they're in the roster. Administering teams for groups projects is a pain in this mode too.
"GitHub Organization", much better for my situation.  Similar to how a company can buy "Organization" configurations from GitHub, these are also available free for educational purposes. It also works even if the student doesn't have the individual "Student Pack" features. So what I've been doing is creating an organization specific to each my course+semester, and requesting GitHub support activate the educational discount.  Once that's done (which usually takes less than a day), I can create both public and private repositories within it.  I can also create "Teams" with my students in them, to grant them access permissions.

From a professional training perspective, option 2 is much better because the system behaves exactly like they'd encounter in a workplace using GitHub. I typically create a repository for each assignment, containing any baseline files I want them to have, usually set to Private.  Then I grant the "team" read access to it.  They then create their own fork, which automatically goes in their GitHub account namespace (or potentially in the organization's namespace if you choose to allow that). It will remain private if the upstream is private. Otherwise, they have nearly complete admin features to learn with.  Because their homework repositories are forks of mine, it's easy to find all their work, and they can directly grant access to teammates and use any of the fork, branch, merge, etc. features they should be learning. Also, I and my TA automatically retain the ability to access their repositories (read at least), because they forked from the organization.
The only two bugs or design flaws I've had to deal with using GitHub Organizations for coursework are these:
A. The fork of a repository which has team/collaborator permissions automatically COPIES those permissions to the fork, EVEN when the fork is created in the user's namespace. Thus I have to remind them to REMOVE that team as soon as they fork, otherwise the whole class can see their repository contents. I have not found any setting that disables this unwanted inheritance of permissions.
B. You do have to be careful with permissions. For example, if students have already forked a homework repository and you remove the team/collaborators from having read access to the original one, it will instantly and without warning (last time I checked) DELETE all those forks!

It would seem that hosting your own Git server and providing accounts to students is the best alternative. (By "you", I mean your institution, at least the institute or department, if not the university as a whole.)
Going this route allows the university to ensure the repositories will never become public. Any unnecessary trouble of account creation among students could be skipped, as an account could be automatically created for each student (the same way many universities these days automatically create a self-hosted e-mail account for each student).
Lastly, asking students to register with and put their data on any 3rd party website (that might even be abroad and thus subject to different standards of privacy) sounds dubious to me, at the very least for reasons of privacy, but depending on your jurisdiction there may even be legal obstacles to it.
I have written this answer based on my personal experience of working in an institute where an own SVN (back then one of the best practices) was provided to all students. My experience with such a setup were invariably positive.

A solution one of my professors used was to have herself be the owner of the repo for each team and then just allow each member access.
That way they the students could learn to use Git without having control over whether the repo went public or not; they could write to the repo, but not change its settings.
(There's really no way around the fact that students can still copy files and put them out publicly, somewhere else, however.)

One option is to create your own "github", check out gitlab. There you can define whatever rules you desire. Downside is that it requires a machine and some manpower to keep it up to date/manage it in general.

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Academic Hiring Process and Practices for Junior Professors in Germany
I am being considered for a job in Germany (W1 junior-professorship) and I was hoping to get some insights regarding the process as I come from the US system and am unfamiliar with how things work in Germany.

I notice that the application packages do not require inclusion of recommendation letters. In the US, the typical requirement is that the application package includes at least 3 letters. Will the schools require recommendation letters once selected for an interview or the job? Do letters or references play any significant role at all?
Selection: I know this should vary by case, but how many people do they tend to put on their short list?
Interviews: I get a feeling that the interview process is brief and a lot less tiring than the American system (for a R1: Typically a 3-day campus visit, job talk, endless meetings with professors, deans, grad students, teaching demonstration, etc, etc). What do they focus on in Germany? (I am asking this as I was invited for an interview, but I was not even asked to do a job talk or teaching demonstration) Are there typically multiple rounds of interviews?
Selection committee: That some European departments practically have a one-person decision making body came as a surprise when I first came to Europe. How is the case in Germany? How many people in the department are typically involved in the decision making process?
Final decision: How fast do they move with their final decisions? For example, the job I am considering only has about a four month gap between application deadline and position start date. This is significantly shorter than a typical US-Search where many schools begin examining applications a year before the position start date, and tells me that they should be moving fairly fast with the decision. Any inputs?

I know these might be a lot of questions. As someone unfamiliar with the system, I am hoping to gain as much insight as possible.

I may be wrong about this, but from your question I have the impression you don't know the German system at all, and from that I conclude you don't know the people in the faculty where you are applying. If this is true, I bet you won't get this position. In Germany, you only have a chance if you have a local advocate. If you don't have one, then you may as well forget your application. In Germany, hiring processes in academia are often only show, they only hire people they know. Please tell me when you get informed about the decision. I would be really glad if you told me you did get the job.

You are right that I do not know anything about the German system and you might be right that they won't give me the job (after the hassle of interviewing me, since I got an invite). One thing that might make things different, though, is that I am in a very specialized, yet in-demand, field where there are not that many practitioners that would domestically qualify for the job. That is what got me into Europe in the first place and I am not sure if this department can in fact hire someone within network for this position.

As I said, the hiring process is often only a show. And they need to have candidates from outside the network to make a good show. Anyways, I do wish you get this job, it would also mean the German system is not as corrupt as I think.

@user12956, thank you for your insights and comments. I am wondering if German universities ever have failed searches? Also, if it is a widely known fact that internal candidates would end up getting hired, why would anyone bother to apply for these positions? (or do most people not apply for these positions where they do not have networks?)

@user12956 I'm not disputing that this can (and does) happen, but I wouldn't assume this is the norm. Every committee I've been involved in had members from outside the department as well as from outside the university, for example. It is true, however, that having an advocate on the committee helps tremendously. But that doesn't have to be a personal acquaintance, just someone who really likes your research.

@socialsciencedoc Yes, failed searches do happen.

It's an open secret. Many know it, few say it, never does a professor admit it. That people still apply may have many reasons: it's free to apply, if you get invited you get valuable interview experience, etc. etc.

Typically a 3-day campus visit — This obviously varies by field and institution, because everything does, but I've never heard of a 3-day faculty interview in the US.  (Interviews in my R1 CS department last 1.5 to 2 days.)

In Germany, you only have a chance if you have a local advocate. — In my experience, that's also true in the US!

As xLeitix mentioned in his answer, I do indeed hold such a position, and have also sat in on a search committee (as a non-voting "interested bystander").

1) I notice that the application packages do not require inclusion of recommendation letters. In the US, the typical requirement is that the application package includes at least 3 letters. Will the schools require recommendation letters once selected for an interview or the job? Do letters or references play any significant role at all?

It could go either way, depending on the preferences of the chair of the committee. In my process, my references were asked for recommendations; for the committee I observed, they asked "neutral parties" who could comment on all of the finalists.
However, one thing is absolutely certain: your PhD advisor (or Doktorvater in German parlance) will never be asked to submit a letter of reference on your behalf.

2) Selection: I know this should vary by case, but how many people do they tend to put on their short list?

Typically four to six people are put on the list of interviews, while two or three usually make the final "ranked" list to be asked if they are interested in the position.

3) Interviews: I get a feeling that the interview process is brief and a lot less tiring than the American system (for a R1: Typically a 3-day campus visit, job talk, endless meetings with professors, deans, grad students, teaching demonstration, etc, etc). What do they focus on in Germany? (I am asking this as I was invited for an interview, but I was not even asked to do a job talk or teaching demonstration) Are there typically multiple rounds of interviews?

Typically, there is only a single interview, and it is indeed far briefer than a US-based job or faculty search interview. None of the interviews I've had have been longer than two hours in duration, including any teaching presentations.
The focus in such junior positions is almost always on research, with very limited emphasis on teaching. You should plan to talk about what you've already done, and what proposed work you'd want to start. You'd also want to give some thought as to how you would recruit students (always a challenge for junior faculty in Germany).

4) Selection committee: That some European departments practically have a one-person decision making body came as a surprise when I first came to Europe. How is the case in Germany? How many people in the department are typically involved in the decision making process?

It's not a one-person decision making process, but it's also not a very large group, either. Typically, there will be between five to nine voting members of the selection committee, including the chair, other professors, and possibly students and equal opportunity staff from the university (who can refuse to give permission for the hiring process to go forward if viable underrepresented candidates were not given due consideration).

5) Final decision: How fast do they move with their final decisions? For example, the job I am considering only has about a four-month gap between application deadline and position start date. This is significantly shorter than a typical US-Search where many schools begin examining applications a year before the position start date, and tells me that they should be moving fairly fast with the decision. Any inputs?

It took about six months after my interview to receive an "offer" from the university, which I found rather slow, but having had more experience with German academic bureaucracy, I no longer find that surprising. (I find the four-month timetable frankly overly aggressive, and would expect that the actual start date would be substantially later than their target date.) However, every university and faculty within a university has its own way of doing things, so what might take six months in one faculty might take two months in another.

Very good and comprehensive answer. It may be worth noting that even though the selection committee is usually not small, for W1 positions it would very often be largely influenced by just one or maybe two persons (typically head of institutes/chairs where the position is affiliated).

I have some hearsay knowledge about the hiring process for W1 positions. I will do my best to answer correctly, but maybe aeismail can chime in later - I think he is currently on such a position.

1) I notice that the application packages do not require inclusion of recommendation letters. In the US, the typical requirement is that the application package includes at least 3 letters. Will the schools require recommendation letters once selected for an interview or the job? Do letters or references play any significant role at all?

If they did not ask, they probably don't need / want them. In central Europe, letters of recommendation are not traditionally asked for. Many institutions are now starting to ask for LoRs as they adapt more of an US system, but it is certainly not that uncommon that they did not want to see letters.
As Dirk points out in the comments: instead of letters, the committee will often ask experts in your field for "comparing reports", however, this is not under your influence. You cannot select said experts, and you will never see the result.

2) Selection: I know this should vary by case, but how many people do they tend to put on their short list?

As you say, it varies by case, but traditionally at least 3. Dirk states that his experience is rather "at most 3", often less. Let's agree on three-ish.

3) Interviews: I get a feeling that the interview process is brief and a lot less tiring than the American system (for a R1: Typically a 3-day campus visit, job talk, endless meetings with professors, deans, grad students, teaching demonstration, etc, etc). What do they focus on in Germany? (I am asking this as I was invited for an interview, but I was not even asked to do a job talk or teaching demonstration) Are there typically multiple rounds of interviews?

This varies a lot. I have once applied for a job where they invited people for an entire week. However, a one-day campus visit with a talk, dinner, and some meetings with core faculty seems usual. Again, Dirk says: "Always a research talk, always a job interview, often a teaching demonstration, seldomly further meetings or campus tours, never a dinner.".

4) Selection committee: That some European departments practically have a one-person decision making body came as a surprise when I first came to Europe. How is the case in Germany? How many people in the department are typically involved in the decision making process?

Again, varies a lot. Formally, the decision is usually a committee decision, but in reality the actual power often lies with a single person (either the dean or the head of the institute / lab that the W1 professor would be assigned to).

5) Final decision: How fast do they move with their final decisions? For example, the job I am considering only has about a four month gap between application deadline and position start date. This is significantly shorter than a typical US-Search where many schools begin examining applications a year before the position start date, and tells me that they should be moving fairly fast with the decision. Any inputs?

I have no idea. My impression was so far that the process does often not move very fast, but I am sure there are exceptions. Dirk says that one should be prepared to wait at least a few months, but I guess that is true for every committee decision.
All that being said, I should warn you that the actual job of a W1-Professor in Germany is not very well-defined. Some are actual independent professors with their own group, own money, and own research agenda, but some are little more than glorified postdocs with very little factual independence. My instinct is that if they do not make a lot of fuss about "your" job during the application phase, the position you applied to may fall into the latter category. You would be well served to ask very concretely what your actual working conditions would be.

I have some comments that not make a new answer: 1) LoR are rare, but the commitee will ask experts in your field for "comparing reports", however, this is not under your influence. 2) I would say it is" at most three". I have seen shortlists with less than two but never more than three. In rare cases there will be a shared last place. 3) From my experience: Always a research talk, always a job interview, often a teaching demonstration, seldomly further meetings or campus tours, never a dinner. 5) This is complicated. The commissiom has to wait for the comparing reports (takes at least six

weeks). Then commission forms a shortlist is a couple of weeks. Then things slow down considerably because usually several other commitees have to approve the decision. There can be more than four such commissions and each of these meet regularly but not often - the process of approval may easily take several month (for Juniorprofessor this is usally quicker since less commission are involved). Hence, prepare to wait at least a few month for an official decision.

@Dirk Really, no dinner? In Switzerland we even take out applicants for PhD positions for dinner. We think it's the best way to find out how compatible a candidate is, chemistry-wise.

Nope, there never have been a dinner.

@Dirk I have added some of your comments to my answer.

Thank you xLeitix and Dirk. It is interesting that you say sometimes W1s are no more than a "glorified postdoc." That changes my perspective on things considerably. What would the future career trajectories for those at W1 level be? I read somewhere that it is a relatively new system designed to develop junior scholars, but I haven't heard how it has been working in practice. Does the fact that the positions are non-tenure track mean that those at the W1 stage need to work on habilitations for promotion into actual tenure-track/tenured jobs?

@socialsciencedoc The career trajectory isn't very clear. That's also the main criticism of the system, as far as I know. Tenure-track as such is almost non-existent currently. The basic idea would be that at the end of W1 you can apply for a W2 or W3 somewhere else, but how realistic this is I am not sure.

AFAIK (I'm neither in the position, nor do I have any plans to go in that direction) one of the official goals of the Juniorprofessur is to offer a way to become professor without habilitation. So formally, you do not need to work towards habiliation. Nevertheless, 2/3 of the junior professors  work towards habilitation (see http://academia.stackexchange.com/a/16638/725, where I put also dug out  some statistics about junior professorships and tenure track).

LoR are uncommon in central Europe for any kind of job application. Instead we have the Arbeitszeugnis (http://de.wikipedia.org/wiki/Arbeitszeugnis), which you get when a contract ends. You are basically supposed to hand that in (possibly without the future employer explicity asking for it) - except if you apply out of an existing contract, because then you don't have one. That being said, anyone wanting to hire a Juniorprofessor will know that people from the US have LoRs instead. I think I'd ask them if they want to have LoRs as coming from the US you do not have an Arbeitszeugnis.

@cbeleites I have never seen these "Arbeitszeugnisse" in an academic environment, though. If not asked for specifically, I would never hand those in.

I never handed in an Arbeitszeugnis for academic positions. They are, as far as I experienced, not needed. I also think that @user12956 comment is misleading. I now the hiring process from both sides and this is not how the system works.

@Dirk It is sometimes like that.

xLeitix and @Dirk: fair enough - coming to think of it, I'm probably wrong: People at my instute get them but we're a research institute, not university - though we work like a university institute. I didn't have one when I started as I also came from a foreign country.  Actually, I don't even have any close colleague who could have had one: they all are either PhD students fresh from university or postdocs who came from foreign countries. I assumed that I was not asked because they knew I wouldn't have one, but maybe this applies to most of us, so there's no sense in asking...

@Dirk A nitpick: Since the OP has not yet given his talk, he is likely still on the long list (whose size is usually about twice that of the short list, meaning four to eight, depending on how narrowly the position is focused). The (ranked) short list of two to four (sometimes ex aequo) will be made based on the talks, interviews and expert reports (usually in that order, i.e., a subset of candidates from the long list will be refereed, and a subset of that makes the short list).

You are wrong, Dirk, never say never :) I've been on search committees where we invited the person (from the States) whom we REALLY REALLY wanted (based on his research) to dinner. He accepted the offer, and then quit on short notice when he got a better offer.

@cbeleites: "I don't even have any close colleagues who could have had one; they all are either PhD students fresh from university" - I even got an Arbeitszeugnis for my "Zivildienst" (substitute for military service), which I did before entering university. And I guess internships while studying would be another opportunity to get one.

@O.R.Mapper: I'd say Zivildienst is closer to a normal job than a PhD contract. Normal, say, kindergarden staff clearly gets them, and so do interns. My guess is that the staff office will prepare something  whether you are Zivi or "normal" staff or an intern. I have Arbeitszeugnisse for student jobs I did while studying, and I guess I would have had the right to ask for one at university (the more so as I was paid for teaching, not for the PhD research). Just at university, noone ever thought of it. Maybe because the degree is kind of a Zeugnis as well.

@cbeleites: My Zivi position was not managed by HR (but by a special office for Zivis and volunteers), whereas my Arbeitszeugnis was written by the doctors at the place where I worked. Don't know whether that is an unusual observation. In any case, my point was that it's well possible to have Arbeitszeugnisse even for people who are "fresh from university".

I applied for a similar position, coming from the UK. Here's my experiences to add:

They didn't require letters of reference
Interview: 1 day: presentation / teaching / research
Timeline:
application deadline
2 weeks: invitation for interview
2 weeks: interview
8 weeks: received offer letter
8 weeks: start of employment

Wow, that's quick! Good to hear that this is possible in Germany.


text:
Do A+ grades (as an undergrad) matter at all for graduate school?
If I get A+ grades then it will raise my GPA in my undergrad institution, as well as for Columbia which is where I want to go to graduate school for statistics. Should I try hard to get A+ grades or should I be content with As? Trying for A+ grades would not cut into any of my important academic activity such as research or my other classes because I already make all As, but it might slightly affect sleep and socialization.
Edit (from answer): To be clear I am an undergraduate right now.

In my experience, grades matter early on when you apply for scholarships and don't have any publications yet to speak of. The longer in you get, the less important they become, much like almost anything that you do after your graduate.

Are you interested in a PhD or a masters? I'm not sure I'd recommend the columbia stats MA program....

Why the downvotes? This is a perfectly legitimate question, in scope for this site, even if the answer is obviously NO.

If you have any sleep or socialization, you are clearly not ready for graduate school.

I would say it depends what field you are going into, as some grad programs have more qualitative criteria for selecting candidates; in the humanities and social sciences, your cover letter, research proposal, CV,life/professional/creative experience and an interview can matter more than GPAs, especially with so much grade inflation everywhere. I know people who got into fully-funded master's and PhDs with Fs on their transcripts which they were able to justify in their cover letters and/or interviews, and I also know of people who didn't get in (particularly in med school) for having a few C's. Can you be more specific about the kind of grad school you have in mind and what you know of the evaluation criteria?


text:
Is it common to include foreign terms in the title of a thesis?
I'm writing a cross-language thesis. In other words, my thesis is about a foreign culture.
Is it common to include foreign terms in the title of a thesis?
If yes, should I include the translation of the term (in parentheses, for example)?

A title with parenthetical explanations would feel very clunky, to me. (Admittedly, I'm not in a field where this sort of thing would crop up.)

Could you please tell us what is your field?

Theoretical computer science / mathematics, where you'd just use the English name for everything, if you were writing in English. You don't find mathematical constructs that have a name in one language but not in another so the issue you're facing doesn't come up.

In anthropology, it's pretty common to use local terms in both the title and subtitle. Almost everyone romanizes the terms rather than using the native script. And they leave explanations and glosses to the body of the dissertation itself.
That being said, when it comes time to submit to a book publisher, they're more hesitant about local terms in titles. The issue is that they are legible only to people who already know the local language or culture, so you've automatically limited the appeal of your book. But there have been some notable exceptions:
Travesti : Sex, Gender, and Culture Among Brazilian Transgendered Prostitutes
Toms and Dees: Transgender Identity and Female Same-Sex Relationships in Thailand
The Soul of Anime: Collaborative Creativity and Japan’s Media Success Story
In the examples above, the exceptions prove the rule by either being obvious to English speakers ("travesti" =? transvestite?), close to English ("Tom" is obvious, "Dee" adds an element of curiousity), or already a loan word in English ("anime").

In your first two examples, the subtitle is perfectly comprehensible standard English and largely explain the title anyway and I think that's what proves the rule. You don't need to notice that "travesti" looks like "transvestite" to understand the first title, for example.

Should it be put formatted differently, in italics or between inverted commas, for example?

People use both. Italics is confusing when the title of books are usually italicized, which means the foreign terms get un-italicized.  Inverted commas and quote marks can get typographically ugly.


text:
Can I switch grad schools early in MA?
I am currently almost one semester into a graduate program at a school in Michigan.  However, I just heard back from my dream school in Florida. Am I able to stop my program at one school and start at another?  I don't even mind starting fresh seeing as I'm only 2 classes deep into my MA.  Any help/suggestions/opinions will be greatly appreciated!

I don't understand the question.  What's stopping you?

@JeffE while I agree with your sentiment that there is no reason not to switch (especially from an MA program), I think it is a reasonable question.

You can do whatever you want.  If another school accepts you into their program and you'd rather be there, I don't see a problem.  Of course, there exist circumstances in which switching might have downsides, but you haven't told us enough about your situation for any of us to judge them.  Sounds like you just want someone to tell you it's OK to switch, which I'm fine with doing.


text:
What is the volume of this article in a journal?
I have this line about the article:
BioMedical Engineering OnLine 2007, 6:16 doi:10.1186/1475-925X-6-16

I think the volume is 6.
Then what is 16?
How should you correctly cite the Bibliography in Tex?
My BibTeX
%
% Published abstract
%
@ARTICLE{vladimir,
    author = {Kudriavtsev V, Polyshchuk V and Roy D L},
    title = {Heart energy signature spectrogram for cardiovascular diagnosis},
    journal = {BioMedical Engineering OnLine},
    year = {2007},
    volume = {6:16}
}

I am suspicious about the author and the volume field.

It is volume 6, article number 16.

As others have already said, it's an article number.
You can verify on the publisher's website that papers in the same volume have indeed consecutive numbers.
As far as I can tell there is no bibtex field for an article number, so you'll have to work around it. Personally I'd go for volume=6, number=16, and no page field (it's not mandatory for an @article). The publisher's own bibtex file (go on "download reference" from the article page linked above) reads VOLUME = {6},NUMBER = {1},PAGES = {16} instead; that said, publishers' bibtex files are often quite bad, don't take this for an authoritative answer.
More importantly, the formatting of the author field is wrong. It should be Kudriavtsev, V. and Polyshchuk, V. and Roy, D. L., or even better (if you know their names) Kudriavtsev, Vladimir and Polyshchuk, Vladimir and Roy, Douglas L.. Note that the correct format is surname, name or surname, n., with "and" as the author separator. What you wrote would be parsed as two authors, one with given name Polyshchuk V and surname Kudriavtsev V, and one with surname only Roy D L. Abbreviations and sorting could go wrong with such a field.
For more information on formatting .bib files, ask on http://tex.stackexchange.com.

So the publisher uses the pages field for the article number. This is what I'd also recommend. Some citation styles don't even display the number field, since the issue is usually not important to know. But the article number is a crucial bibliographic information.

From the title, it seems that the journal is an online only journal. Many such journals don't use page or issue numbers, since there is no need for these in an online journal. Instead, such journals number articles subsequently as they appear throughout the year. In conclusion, it seems that in your case, 6 is the volume number, and 16 is the article number.
For BibTeX entries, I usually use the pages field to enter such article numbers. The reasoning behind it is that, in classical journals, page numbers are used to refer to an individual article, while in online journals, it's the article number which takes this role. Also, there are several BibTeX styles which use a citation format with <volume>:<pages>. For these, using the pages field for the article number will be compatible and will turn out as you show in your citation:

BioMedical Engineering OnLine 2007, 6:16

That notation is standard for volume and issue no. For instance, the following is a ACM citation for one of my journal articles:

Jeremy Birnholtz, Shion Guha, Geri Gay, Y. Connie Yuan, and Caren
  Heller. 2013. Cross-campus collaboration: A scientometric and network
  case study of publication activity across two campuses of a single
  institution. J. Am. Soc. Inf. Sci. Technol. 64, 1 (January 2013),
  162-172. DOI=10.1002/asi.22807 http://dx.doi.org/10.1002/asi.22807

If you will notice, after the name of the journal (JASIST), there is the notation 64,1. It refers to volume 64, issue 1.
In your particular example, which I found here, on the top right hand corner, volume 6 is clearly mentioned. The structure of the citation leads me to believe that it is issue no. 16.
In BibTeX, issue no's are default. There is nothing particular that you have to do.
After perusing your author field, they also seem to be well aligned with the actual article. What are your suspicions?

My suspicions are that if I include too much unnecessary pieces of information. For instance, the issue number 16 in the volume field too, and all authors with letters to forenames in the Author field.

I would wager that the issue no and the names of the authors as they are, in the BiBteX are not unnecessary pieces of information. Rather, they are necessary and should be an integral part of any citation system be it IEEE, ACM, APA, MLA etc.

But you do have to include the "issue = {}," tag in your BibTeX file! Also note that many journals do not include issue numbers in citations.)

As per the bibtex documentation, the field type @article has four required fields: author, title, journal, year. All the rest is optional.


text:
Acknowledgement of submission to the Annals of Mathematics
Does the Annals of Mathematics always to reply every submission within a few days? I submitted a few times to them before, and every time I hear back from the  editorial office very soon (within three days). But this time there has been no response to my submission for more than one week.
Is this normal? Or I should inquire about the status of my paper?

Thanks so much, J. Zimmerman, for polishing my english. I am not a native english speaker.

A week is not so different from three days, especially if that week includes the July 4th holiday in the U.S.  If several weeks pass and you still have been given no indication that the paper was received, then it would be worth asking if they got it, but in the meantime I don't think you need to worry.

Did you look at the OP's questions on math.SE by any chance?  I have to think that if you send too many papers about elementary proofs of special cases of FLT to the Annals of Mathematics, then at some point they will stop responding.  I am a bit torn as to whether or not to advise the OP on this.

@PeteL.Clark: Hmm, good point (I hadn't looked at them).  I don't know how they would handle it.  I hope they would suggest the papers were inappropriate and ask the author to stop sending them, but perhaps they would expect people to take the hint if their papers were repeatedly rejected without refereeing.

Thanks for responding. I am afraid sending too many elementary proofs of special cases of FLT is not the case, but a reasonable, rational guess from my question asked.

Moreover, I am a bit torn as to say this: inferring the motivation or background of a post is unsolicited.

@Brian But it might in fact be relevant here. You say you have submitted to them a few times before, but it is clear from your MSE questions that you are not at the moment producing mathematics of anywhere near the quality they expect at the Annals (being one of the very top journals of mathematics). Thus, it is not out of the question that they have put you on some sort of "ignore" (though I have no idea if this is something they would actually do), and this might explain the lack of a reply.

Hi Tobias (if I may call you Tobias), thanks for your kind words. You are right.  I can understand the point if asked this way (that to answer the question necessitates more information). It is my fault that I did not specify the expected answers. In regard to this question, experience-sharing is preferred to submission-counseling.


text:
What exactly is an "unpublished paper"?
In applying to the NSF postdoctoral fellowship for mathematics, the instructions include the following paragraph for the biographical sketch:

A list of: (i) up to five products most closely related to the proposed project; and (ii) up to five other significant
  products, whether or not related to the proposed project. Acceptable products must be citable and accessible
  including but not limited to publications, data sets, software, patents, and copyrights. Unacceptable products are
  unpublished documents not yet submitted for publication, invited lectures, and additional lists of products. Only
  the list of 10 will be used in the review of the proposal.

My question is what exactly does "unpublished" mean? Is a paper uploaded to the arXiv but not yet submitted for publication in a journal considered "unpublished"?

I would interpret "published" to mean exactly what the text says — citable and accessible.
ArXiv papers are both citable and accessible, and therefore do count as acceptable research products.

in general, I would agree with you and count arXiv papers, as well as any self-published paper, as “published”. Yet, in these instructions, they explicitly write “not yet submitted for publication”, which I interpret as they meaning “not published in peer-review journals”… (because “submitted for publication” does not make sense in self-published or arXiv context)

@F'x I disagree. Why do you think it doesn't make sense? ArXiv explicitly uses the word "submission" in their online forms. The process of "submitting" a manuscript to arXiv looks exactly the same to me as submitting it to any journal which has an online-only pipeline. Then a moderator takes a look at it, and if it is not blatantly outrageous it is circulated the next day. And yet, unfortunately, if we believe this recent article, this might still be more than what some journals do for a peer review.

@FedericoPoloni because there is no peer review process for an ArXiv publication.

NSF explicitly changed its reporting requirements from "publications" to "products" a few years ago. Open-source software projects, data repositories, textbooks, and even blogs are considered acceptable research products, despite having little or no peer review. But even before this change NSF happily accepted arXiv papers as publications for reporting purposes. They really don't care about peer review as much as public dissemination. Also, applications for the NSF math postdoc are reviewed by mathematicians, who are generally natives of preprint culture.

Of course, you should ask the program manager to be sure.  Sadly, that's currently impossible.

@JeffE: Mathematicians certainly are comfortable with preprints, but in my experience we're careful to distinguish them from publications (i.e. in peer reviewed journals).  (Source: I am one.)  I would think if they were acceptable here, the instructions would use the word "preprint".  I agree that it is ambiguous, however, and I would welcome an official clarification.

NSF has an official FAQ for their proposal guide. One of the entries in the FAQ is applicable here.

Instructions for the Biographical Sketch Products section indicate that “acceptable
products must be citable and accessible.” Accessibility may be difficult to
accomplish in the case of manuscripts submitted or accepted for publication and
other documents and materials. Access may need to be provided through
organizational or personal websites. Will that be sufficient to meet the proposal
submission requirements?
The requirement that all products be "citable and accessible" is not a submission
requirement, in the sense of blocking a proposal from consideration, but a definition of the
standard to which proposers should adhere. PAPPG Chapter II.C.2.f(i)(c) also notes that
full citation information should be included where applicable and practicable. References
to organizational or other websites are allowable, provided that the site is available for a
reasonable percentage of the time.

From this statement, it is clear that NSF would consider a preprint server to be a reasonable place for a work product to be located. In fact, the key consideration seems to not be citation per se (you can cite pretty much anything), but simply having a clearly defined "thing" that is readily accessible for the review committee to inspect.
Given this statement and the confidentiality of peer review processes, it is next important to observe that there is no way for a proposal reviewer to distinguish between:

A preprint that has been submitted
A preprint that has not been submitted
A preprint that was submitted at the time when the proposal was written, then rejected before the proposal came up for review.

Between this and the shift to a general definition of "work product" it is clear that NSF is trying to give as much latitude as possible for the review committee to say "this person is doing interesting work, let's give them a fellowship." It would make no sense for a committee to be allowed to consider a non-peer-reviewed software repository on GitHub but not a non-peer-reviewed preprint on arXiv.
Bottom line: material on preprint servers is fine to include in an NSF biosketch.

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


text:
verbal agreement to convert masters to PhD but reconsidering
I am currently doing a Masters of Philosophy, with my key interests being ecology and evolution.
When I enrolled earlier this year, I had an agreement with my professor that I would continue to a PhD. Unfortunately in the first two months, my first project fell through to lack of funding. My professor then showed me another project I could do. This project is very similar to my honours research...in fact, it is almost exactly the same, with very few new techniques included. I had a few weeks to think about if I wanted this project, but did feel a bit of pressure to make a decision. I decided to continue with this project despite my reservations.
My main issue now is that I have realised (at 5 months) that this project, while interesting, isn't going to get me a job when I finish. While I am doing some lab based work and doing some phylogenetic analyses, I'm not doing any of the field work or statistical experience that I need to be competitive for post-docs.
I've considered reworking my project, however I've had a number of concerns about it. First of all is that my supervisor doesn't seem keen to rework it to a large extent and doesn't seem to understand the time it takes for me to read and analyse papers to determine how to change my project.
The second issue is that no one in my lab is an ecologist, statistician or evolutionary biologist (primarily genetics and bioinformatics) and I will not be able to get the support I'll inevitably need down the track. The final issue is that I am getting no funding. My supervisor is paying for my labwork, but I am not able to conduct more field studies or more complex genetic analyses because we can't afford it.
I've sort of come to the realisation that this isn't what I want from a PhD. The only issue is I have a verbal agreement to change to a PhD at 1 year into my masters. I love my supervisor and the lab, so don't want to burn bridges by changing my mind on them. I also feel guilty as my supervisor is paying for my lab work, and I don't want to put him out. I am just stuck as to what to do in this situation, and how to bring this up with my professor without ruining my chances of working with them later or affecting my relationships with them.
Basically, this can be summarised as: I don't want to do this PhD project and would like to keep it as a masters, but am not sure how to go about discussing this with my supervisor, and am not sure how it would impact me if I decide to do a PhD in the future.
Has anyone been in a similar situation and can offer advice? Is there a way to do this without impacting my career as a researcher, or my relationships with my lab mates and supervisor?
I would love any advice you have on this because it's really distressing me!
Thanks

There's a lot details really narrowly tailored to your specific situation. What is your question exactly?

Basically, this can be summarised as: I don't want to do this PhD project and would like to keep it as a masters, but am not sure how to go about discussing this with my supervisor, and am not sure how it would impact me if I decide to do a PhD in the future.
Has anyone been in a similar situation and can offer advice? Is there a way to do this without impacting my career as a researcher, or my relationships with my lab mates and supervisor?

I don't think you need worry too much about offending your supervisor.  People leave grad school for all sorts of reasons all the time, and your supervisor will surely know this from experience.  Your reasons sound completely understandable.  He must also know that a student who doesn't want to be there is unpleasant for everyone.  Seeing as you're staying on for a masters, you should have plenty of time to wind up your project in an orderly way.  He might be disappointed, but I can't really see it harming your long-term relationship.

If the question is "how to tell my MS supervisor I've changed my mind about doing a PhD with him," seems like a duplicate of this question

I don't want to do this PhD project

If you don't want to do this project, DON'T DO IT. PhD is not everyday fun and it is sometime harsh to keep motivation through the ups and downs.
About your adviser, I will not be too worried for him/her burning bridge. How many PhD student actually drop during the PhD. As Nate Eldredge said, It is quite bad for an adviser/group to have an unmotivated student. Moreover you haven't yet start the PhD. It will be much worse for you adviser if you start and quit after 2 years because you cannot stand it anymore.
As often, you should just be frank with your adviser. Explain this is not the project you are ready to invest 4 years in your life and if he/she has a minimum understanding, it should be fine. If you are not at ease, do it in several discussions, where first you express your doubts on the current project. I think any adviser hearing that should actually advise you to not continue with a PhD.


text:
Should I cite all R packages I used?
Intro: R is a open-source software tool for statistical analyses and graphics, which is heavily used in different science disciplines and which is becoming more and more popular (although it is already quite popular in many areas). In addition to the base version, people from all over the place develop so-called packages, upload them, for example, to CRAN, where they can be freely downloaded to use.
Q: I am writing a manuscript for a peer-reviewed psychology journal and used a lot of R packages in my work. Of course, I want to and will cite R itself and the packages that I relied on heavily (e.g., to simulate or analyze data). However, I have also some packages, of which I used only a single, little function. For example, I used the odd function from the gtools package to determine whether an integer is odd or even. As far as I can see, the function is only a single line long, and I could have written it myself (but I didn't!). On the one hand, I want to give credit to these developers, on the other hand I don't want to blow up my reference list and confuse readers. So the question is, should I cite every single R package I used?
BTW: Note that R has the nice function citation("some package") to access citation information provided by the package authors; see also citation() to cite R itself.

Citing R and its packages (in the light of the answers below) would support the development of such great, yet free of charge, open source tools.

Overall, I would suggest you err on the side of rather citing too many packages (with version numbers, please!), although odd quite probably is a borderline case. I'd rationalize this tendency as a bit of balance for all the people who use packages extensively but do not cite them.
In general, I would certainly cite anything that saved me a non-trivial amount of own work (as in, "I could have done this myself, but it would likely have cost me half a day").
The length of your literature list should not really be a concern in the days of PDF publishing. And "we used R [3], packages foo [4] and bar [5] as well as multiple helper functions [6-10]" should not be too confusing to your readers.

You should cite everything you use. Maybe many won't do it because they just use too many packages. This shouldn't hinder you from citing. So here's how to cite multiple packages at once:
https://blogs.ethz.ch/mylifesciencejourney/2017/07/14/cite-multiple-r-packages-at-once/

Unfortunately, there is a practical limit to this strategy in some cases: at least in my case, there are still a lot of page limits around, which severely limit the number of references one wants to give in an article...

@walls: That link do not work.

YES.
There are lots of reasons to and no reasons not to (unless you're under some kind of strange space/ink constraint).
Here is an important and under-appreciated reason why:
Most of the people who make the kinds of R packages, in fact the people who made R itself, are other academics. Meaning: They didn't get paid specifically for the time they spent making lme4, ggplot2, stargazer etc. Software development is very unappreciated in academia. Imagine spending a lot of time writing and maintaining a package that is used by thousands of people in your field and then being asked by a tenure/promotion committee why you didn't write more papers or do more experiments. It's very difficult to get someone who isn't a user (or even a software-minded person) to properly appreciate the time and skill involved in making good software.
The only way to convince university systems and leaders that the work you spent writing that software is to show them in a way they understand, that means citations. They're not going to care about your Stack Exchange reputation or how much juice you've got on GitHub, they need something Scopus can compute and they can itemize and count.
Much of the workings of academia is based on beans. Much of the effort at universities is dedicated to counting and managing those beans. How many students are in your program, how many grants are awarded, how many Ph.D. defend, and how many papers are published and cited are all very important beans which decide who gets resources. It would be sad indeed if someone who wrote a useful R package didn't get the credit they're due and thus be allowed to make more wonderful tools. Imagine if Hadley hadn't started working for R-Studio, he might be standing in front of some committee someday asking him why he spent so much time writing "software" instead of "papers," or trying to explain why he can't take on a third course this semester because the dept chair doesn't understand that writing software is something that actually takes real time.
Also consider this:
Most scientific papers are cited fewer than 10 times, if ever. A reasonably useful R package is likely to impact many more people than any "real" publication, but that person gets no credit if you don't cite it.

I very much agree with the importance of citation to generate measurable numbers for science administration. I develop packages and yes, it is important to be able to justify the effort - the more so if your institute is still rather reluctant about open source (not to speak of open data...). In my field pointing out how many people cite the package is an important and easy to gather number. This is IMHO even more important for small niche packages than, say, for ggplot2. (Nevertheless I also cite the packages I use "only" for graphical display etc).

Absolutely! Citations are free, and they are a blessing to the creators of those packages.  Unless you're held to a strict page limit, there's no reason not to have a "methods" section in which you list all of the packages you used.  It can be a single sentence.  If you want to give pride of place to a few key packages that your work relied on, then give them a sentence each, but don't snub the others.  Some day, you'll be happy when others cite your work.

There's no definite answer to this, but here's what I do.

I cite R itself and the packages I need to perform the actual analysis I report in my paper. I do not cite packages I consider to provide various tools (graphic tools, mathematical tools, etc.). The line between these can be difficult to draw sometimes, of course.
Always, always make your data and your code publicly available. You need to make sure that other people can replicate your result. Other people can also see there what packages you have used.

Ok I realize this thread is 6 years old. So sorry for digging it up. However, maybe my routine is helpful to somebody else as well.
I usually do it pretty similar to Sverre, and cite in the main article R and the most important packages for my analyses. However, in addition I cite all packages in a table in the appendix with 4 columns (packagename, version, maintainer, citation).
Here is a small but useful snippet for this purpose. It creates a data.frame with 3 of the 4 mentioned columns and a .bib file with the required citations. Some manual work is still required (e.g. copy the .csv table into your word / text program and import the .bib to your citation management tool) to finish the appendix.
The snippet still saves me a lot of time.
# Export Citations as Bibtex (.bib)
write_bib(file="Bibliography of packages.bib")

# Table (.csv) with all information on the packages
appendix_packages <- data.frame(Packagename = character(),
                                Version = character(),
                                Maintainer = character())

require(pacman)
for (pkg in p_loaded()){
  appendix_packages <- appendix_packages %>% add_row(
    Packagename = pkg,
    Version = as.character(packageVersion(pkg)),
    Maintainer = maintainer(pkg)
  )
}

write.csv(x = appendix_packages, file = "List_of_packages.csv", row.names = F)

Edit August 2022
Disclosure I am the maintainer of the datscience R-package.
As I used this function so frequently, I also included the Rcitation_appendix() function in the datscience package: Documentation Website, Code
Usage:
library(datscience)
library(lavaan)
Rcitation_appendix(filename="Appendix A - All R packages utilized.docx")

This creates a folder called 'Appendix' in the current directory and places two files in it, a .docx word file with the table and a .bib file for your reference manager. I later on manually enter the references in the most right column (Citation)

the dataframe "appendix_packages" does not necessarily need to be exported, one can also directly turn it into a latex table via kable (see also this answer)


text:
Is there an easy/good way for professors to connect with corporate consulting projects?
I'm not an academic (sorry!), but at various points over my career I have been interested in working with professors on a variety of projects.  I never found an easy way to find a professor who might be a good fit (e.g. is in the right field and interested in consulting work) and I'm wondering if there is one?  I suppose that part of my question is whether professors in general are interested in consulting work - I know they are extremely busy, so I'm not sure if this type of work is even attractive.

As with any consulting, if the price is right I'm sure you'll find some interested professors (though not all of them).

Possible duplicate of: http://academia.stackexchange.com/q/11715/10643

@CapeCode I think question is different in that this asks how to find profs who want to consult where the other is about how to handle the initial stages of the meeting/relationship. That said, the answers at your link would likely be helpful to the OP.

I am one of the founders of a company that does exactly what you are asking.  It matches professors and businesses together for consulting and executive education.  The company is called LIFTPhD.

This type of work can be very attractive.  Some universities even encourage it.  I'm entitled to spend up to 20% of my time on consulting projects.
It does get tricky.  The prof involved should really be using ZERO university resources for consulting work.  While it may never come to it, this should be verifiable through an audit if that's ever demanded. My own Univ Policy is "Faculty members may not use facilities, equipment, materials, funds, personnel or
similar resources of the University in the consulting activities. They may use
University telephones, email accounts, computers and software programs that are
generally available to the University community, and library resources (but not library personnel), so long as the use is reasonable in duration and frequency, does not compromise the security or integrity of University property, information or software, and does not violate any other University policy".  Such policies may vary by university or country, but if I were hiring a consultant, I'd pay ample attention to making sure the university involved did not get hooks into any of my IP.
This can go the other way, as well.  There was a recent court decision (perhaps someone can help me point to it) where a faculty consultant accidentally signed away university rights!! In response, my own school requests that faculty run consultancy contracts through Univ. counsel.  They can't make us do that, but in return they will keep an eye out for the best interests of their faculty as they review the contract.
Finding the right consultant can be tricky.  You don't mention what sort of consultant you're looking for, but I'd suggest looking at web pages of local universities to see if any faculty research interests line up with the work you need to have done.  Start with the departments that produce the types of students that you'd consider hiring to do that sort of work.  If you can't find a match, an email to the chair might help.  In fact, the chair would know which faculty members would benefit from expanding their portfolio in this way.
As with any consulting arrangement, spend some real time on the contract.  Make sure the consultant understands what the deliverables will be.  A good consultant will not take on a poorly defined job, and should be able to help the costumer define the job.  If the job is vague, consultancy may not be the best way to go, and you might consider sponsoring a small research project.

The prof involved should really be using ZERO university resources for consulting work this varies greatly between institutions and countries.

@CapeCode good point, but it's still something I would demand as the person hiring if there were ANY concerns about IP, or I'd get it in writing from the university that the university has no claims over the IP.  I know my employer "requests" (as they can't make) us run any contract through their counsel just to make sure that the contractor isn't signing away university rights (as made famous in recent court case).  I'll edit a bit

While it is often a little bit challenging to set up - how consulting works will vary by institution, position, etc. professors are often greatly interested in doing consulting work. Just like industry experts, it allows them to make more money than they otherwise would, work on some interesting projects, etc. It's also, if you don't necessarily need "Professor So-and-so" but merely a highly trained expert in the field, a good way to help supplement grad student and postdoc income.
The best way to get in touch with them is to find someone who seems appropriate, and ask them. There are a couple ways to potentially find someone:

Look at your local university. Physical proximity can be helpful, and even if they don't/can't work on a project at the moment, they may be able to point you in the right direction - they know the field better than you do.
Try to find academics who clearly do work in your field. Are there papers you've read, either in the mainstream press or journals, that are relevant to your problem? Is there a particular university you hire a lot of graduates from? etc. Again, this may not prove immediately fruitful, but could help get you oriented.
Professional organizations may be able to help. They often have job boards, membership directories, etc. At least one I've encountered also actually has it's own consulting service - it essentially collects interested members, and matches them with projects as needed.

re 1 above: quite a few unis have "experts databases" or "media contact" databases that can be very helpful in finding people in the right field.