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Can a researcher hire 100% themself with funds from H2020 project (or other call)?
Once in some conference I heard that some guy was working as researcher (PI in different projects) at some university in Italy, but he had no official position. I understood that somehow, before entering this university he applied to an H2020 project (no ERC, StG, CoG, or AdV) that he got and that in the conditions he put in the budget 100% of his salary. So he kind of hired himself. Then he was always applying to H2020 (or other) calls in order to get continuity of his contract.
I wonder how this works.

The answer seems specific to a given university's policies and asking for a list of other universities seems like a shopping question. Both of these questions types are off topic on this site.

I edited then my question

Asking about similar situations is also "shopping". Please see this link: https://academia.meta.stackexchange.com/questions/3657/why-was-my-question-put-on-hold-for-shopping

Broadly, your question seems to be abound funding yourself entirely with soft money. There are already several questions on that topic on this site: https://academia.stackexchange.com/search?q=soft+money

I am closing this question as unclear, because you already described the process and do not specify what you are skeptical about or similar. The answer also seems to have interpreted the question differently than you.

It's quite normal for people to pay 100% of their salary (or the salaries of researchers, post docs, etc) out of H2020 project grants. I'm not following what you see as the problem. It just means that person spends 100% of their time on that research.

I do not see this as a problem, the other way around! It is because I am thinking about moving to other University, where there are currently no positions offered, but using this mechanism. What I do not know exactly are the details.

The exact details will be different for every situation. It's unlikely that you can successfully get any H2020 funding without a university affiliation, but if you have a good relationship with where you want to move they may support you for the application, offering the EC assurances that you will be hosted if you get the funding. Or you might have a formal affiliation with no contract with that Uni already. Or, finally, you might apply from your current location and once you have the funding, switch institutions but that only works...

...if it is money that comes with you (e.g. an ERC grant) rather than money that is awarded to your institution for you to work on (e.g. most H2020 grant contracts)


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Find articles that share datasets and code
I am working on some project, in which I would like to find articles where they use some computer code to treat data, and the used datasets and code is totally available (github, personal website, etc). So I go to Scopus, Google Scholar, ISI Web of Science, etc, but I do not find a good strategy for this purpose. I try to add keywords to the search like "code available" or "github", but it does not always yield accurate results. I also know that some journals force papers to give datasets and code, but do not know how to find these exact journals in my domain. So, what is the best strategy for finding articles that share code and datasets?

https://paperswithcode.com/. It contains the publications and the corresponding code. Most top computer science conferences ask for relevant supplementary material, which includes code. Many papers (atleast in Computer Vision/Machine Learning) which are published in top venues contain links to the code as well.

Many professors also maintain public git repos, which contains the code for their publications. You can search on Github or go to the homepage of the professor to find the link.

You can also email the author directly. In my experience, many are willing to share it.

What field are you in?

try github search

paperswithcode.com.
It contains publications and the corresponding code.
Most top computer science conferences ask for relevant supplementary material, which includes code. Many papers (atleast in Computer Vision/Machine Learning) which are published in top venues contain links to the code as well.
Many professors also maintain public git repos, which contains the code for their publications. You can search on Github or go to the homepage of the professor to find the link.

Journal of Statistical Software and R Journal both require replication materials for all papers.

zenodo.org is a repository that enables one to index code hosted on Github. Most probably you would find a Zenodo DOI associated in the supplementary material. If not, I've seen some journals like RSC Analyst, putting the link along with the research article on their site.

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Resources on how to overcome writer's block, especially for non-native English speakers?
One of the issues we have at my English-language institute is the problem of getting our doctoral students to write papers in English. For some, writing isn't a big challenge. For others, however, the process is about as pleasurable as pulling teeth or a lobotomy (without the benefit of anesthesia).
What we've found is that there are a few problems that tend to creep up:

Students don't know how to commit their ideas into paper
Students are afraid of writing poorly, so they don't write at all

What I'm wondering is if there are any resources available that can help—particularly international students—with overcoming the "academic" version of writer's block.

Of course there are plenty of resources about how to overcome writer's block, however for different people different techniques work. The advices I always found very useful as a PhD student (although I cannot find the original sources, it's been years) were these:

do not aim high at the beginning. Crappy and hasty first draft is perfectly fine, iterative improvement will come later: as the author here points out, inexperienced writers tend to have too high standard on themselves. Since I am in a formal field, I therefore refrained to start with the paper's motivation, but rather tried to work out the mathematical flesh first. That one is easier in terms of language since the form can be copied/learned from good papers of others. But this differs across disciplines.
block time every day for writing and do nothing else at that time, even if you should stare at a blank wall: this is my way to kill the procrastinator in me. Simply three hours every day a week for writing. Even if during that time one would really just stare at a wall and write nothing, it's better than procrastinating. Eventually the boredom is so high that writing becomes welcomed activity. It is imperative not to do anything else, especially not to study, read or otherwise consult any literature, also get disconnected from Internet and colleagues, etc. The best for me was to go for this to the department's library where was no wifi connection. I read somewhere that this technique is used by some novel writers, but can't find any source of this advice.
Another powerful technique is use public commitment wisely: that is, publicly commit to delivering an artifact at a precisely specified deadline. E.g., first draft of the paper next Friday. Tell to your boss, tell to your office-mate, whatever. The higher the authority you tell, the better. For many people this has a magic effect, because we tend to value our commitments, however painful it sometimes is to stand up to them.

But again, different techniques work for different people.

Well, it's the internationalization aspect that makes it more challenging. Writer's block in a "foreign" language is, I suspect, logically even tougher to deal with than in one's own mother tongue.

+1 for "don't aim high at the beginning" — Experienced writers also tend to set too high a standard for ourselves.  Sorry, I mean, for themselves.  Give yourself permission to write badly; revise later.

@aeismail: as a non-native speaker, I do not see any difference in the remedy of the problem. Except the hurdle might be slightly higher for us.

@walkmanyi: The issue is that I'm not sure if there are additional issues for ESL writers. That's what I was trying to address in my question.

Related: https://academia.stackexchange.com/questions/153611/how-to-get-started-with-phd-dissertation-management-humanities/153622#153622

I don't really see this as a problem specific to non-native English speakers. I know plenty of first-language English speakers who are absolutely rubbish at writing.
The problems I've personally witnessed go much deeper than correct use of the language: It's mainly about organizing your thoughts and what you want to say, and then saying it in the clearest way possible. This usually does not involve any in-depth knowledge of the English language. In fact, being too good may make your writing worse.
I use and preach an incremental writing approach which consists of the following steps

Start identifying the one statement that your paper will make, e.g. "here is a new method to solve problem X", or "method X is better than method Y for problem Z".
Once you're clear on what the message will be, write a rough sketch of your paper in terms of the statements you will make. This should be the main story of your paper. Each statement should really only make a single point, e.g.

Solving problem X is very important.
Most people use method Y to solve problem X.
Method Y has this/that weakness.
Method Z avoids this weakness.
Show on an actual example that Z is better than Y for problem X.

At this point you should start worrying about consistency. What you have to look out for is dependencies between your statements, i.e. have you really stated everything you need to state such that I can make the next statement? Will you be using words/concepts/methods before introducing them? It is important that you get these things right at this early phase, where ironing problems out is still relatively easy.
Once you've nailed your story line, you can start fleshing-out your individual statements. Here too, I would recommend sticking to bullet points and making only one statement of fact per bullet. The first statement above, for example, can be expanded as follows:

Introduce problem X.
List several instances of problem X.
Give a concrete example of where solving problem X is important.
State benefits of solving problem X more efficiently.

Here again, dependencies are crucial! Make sure you don't use any information without having given it in a previous statement. Also try to keep dependent statements as close together as possible. Remember that you're trying to tell a story and need to keep your reader on track.
Also, note that I haven't said a thing about sections. It is usually only at this point that I would start placing section headings and grouping different statements. Doing so too early may cramp your story-telling.
You should now have a somewhat complete story-board of what you're going to say, and you still haven't had to worry about how you're going to write it. What you need to do now is turn the bullets into text.
The way I usually go about this is to turn every statement/bullet into a paragraph of text. The first sentence of said paragraph should be the statement, followed by at most one or two sentences either explaining it in more detail or giving an example of what you are saying. If you need an example, almost every paragraph in this answer was written this way.
The final phase is refinement. Your paper, at this points, will probably consist of a large number of very short paragraphs that don't necessarily flow into each other. This is where you start merging paragraphs and using connectors between them, e.g. "Thus", "However", "Furthermore", etc...
This final step is not something you do once, it's something you repeat until your paper looks, feels, and reads like a regular paper. I usually go through a paper with a red pen and fix things by hand while reading, then implement the corrections, and then wait a day or two before iterating again.

In summary, the process I've just described is completely mechanical and does not involve any in-depth knowledge of the underlying language. The only language ability you need is to formulate clear statements. If you do anything fancier than that, you'll risk loosing any reader whose level of English is below your own.
I am very much aware that there are many people who can just sit down and write beautiful, precise, consistent, and easy to read papers. Good for them. For the rest of us, I suggest using the approach I describe. At least it works for me.

As an international student, I have suffered a lot from writing academic papers. I believe It is an advantage to be English-native speaker in the academia. Well, I mean mastering the language not necessarily a mother tongue. Each time I submit a paper, I expect some comments on its english. I remember first time I submitted a paper it was rejected because of what so called bad english on it. Now after five years of writing and submitting and with the help of the supervisor and continuing reading papers, I got minor comments (in most cases its the reviewer style more than the language itself).
I believe it is up to the students, If they want to have a career in academia they should push themselves by reading and writing in English. They will notice their skills will be developed over the time. Also, proofreading ,to know your mistakes, is a good thing specially in the beginning.

Students don't know how to commit their ideas into paper

This is why you should push them. You want them to have successful careers after PhD, this will be very difficult without a good sense of writing academic papers.
Ask them to write first draft and hand it to you. You can comment on it and send it back to them. This is how it worked for me.

+1 For they should push themselves by reading and writing in English. I myself never benefitted from reading those kind of books others recommended. You may learn how to write news reports by reading those books. It's completely different story when you write math/science papers.

Another +1 for proofreading ,to know your mistakes, is a good thing specially in the beginning. The way I write here is, double check before posting, check again after posting, check again withing the 5 minute interval, modify my answers/comments again until it's really too many times and then stop.

Rowena Murray is very good on this:
MURRAY, R., & MOORE, S. (2006). The handbook of academic writing a fresh approach. Maidenhead, England, McGraw-Hill.
MURRAY, R. (2006). How to write a thesis. Maidenhead, Open University Press.
MURRAY, R. (2005). Writing for academic journals. Maidenhead, Open University Press.
Understanding perceptions and fears about judgement (external and internal) and the difference between performance/learning orientations are sometimes useful conversations to have.

Thank you for asking this question addressing what appears to be a sadly widespread problem in academia. I'm an international student (from India in US) myself, and it's been a great boon for me to be able to communicate fluently in English.
Particularly re: international students, our Office of International Students organizes (spoken) English classes, which are free for all international students and scholars. In addition, at Rice we used to have a group of grad students get together for lunch on Fridays and converse in English (this was a registered student organization called 'English Corner', and they had funding from various sources for the lunches). I realize that you were referring to resources for writing as opposed to speaking, but I believe that particularly for non-native speakers confidence in speaking can translate to confidence in writing. In terms of the actual writing process, there are some online resources, such as  Englishforums
As for resources for a more general audience, in certain departments around here I've heard of a thesis-writing class that grad students are required to take for credit. Our Office of Graduate & Postdoctoral Studies has recently been trying to put together some professional development workshops and courses, which often focus on the 'communication' aspect of academia. Another possibility is that the beginning courses in the doctoral program (1st and 2nd year classes) could be made to have a strong (or at least non-trivial) writing component. For example, one might require students to write an expository term paper or something along those lines.
I realize that roughly everything I've mentioned above has to do with resources available at my university, so perhaps my answer consists of 'Here are some resources that might already exist at your university, or might be put into place there'.

I recommend beeminder. It allows you to set goals publicly. If you go "off track", it penalises you in a few ways you can choose (charges you money, posts to your facebook account, ...).
For me it has been very effective to get me to write. I use it according to the following rule: I count writing sessions, where a session is at least 5 words. In fact, most of the time, I will end up writing hundreds of words, and beeminder just forces me to go over the activation barrier and start typing.

There is a strong line in professional writing that suggests that there is no such a thing as writer's block.
Writing for a Journal should be something mechanic, not some work of art that should come from the depths of your hearth, at the end, it is a skill, and a skill that you have to work on.
Many professors are really bad writers, because their own professors were also very bad, there are few writing courses in a grad student's curricula.
These and other very valid points are presented in "How to write a lot" by Paul Silva, I find it to be a very useful book, and full of great advice both for students and professors alike.
Link to the book

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Travel grants for International students in the US?
I am an international student in the United States (originally from India) and have been here for my PhD in Mechanical engineering since Fall ’06. I've attended a bunch of conferences all in the US and Canada and mainly the ASME or APS DFD (division of fluid dynamics) meetings. As I get close to finishing my PhD, my source of funding (NSF) is running low!
As an international student, I find it difficult to find institutions that provide travel grants for conferences in the USA conducted by organizations such as the APS, ASME, AIAA etc. It is also unfortunate that India doesn't have travel grant opportunities for Indians students outside India.
Does anyone have an idea on where I might look? I have two conferences coming up: the ASME Fluids engineering conference in July 2012 and the APS DFD in November 2012 that I'd like to get travel grants for.

Here is a related question on Travel.SE.

@ESultanik Thanks! I had actually already checked this. I should have amended my question in that light. However,this other link provides information generally for CSE students.

Usually the best place to ask for a travel grant is the conference itself. I see, for example, that the APS DFD 2012 meeting had a travel grant program (sure, now it's too late to be useful). Many big conferences have such programs and those that do not may have "fellowships", which give a reduced registration fee for select students.
Otherwise you want to look at framework programs in your field encouraging the mobility of students. It is true that it might have been easier if you were actually located in India, because of binational exchange programs and such, but you also have to realize that the travel costs would then have been greater!

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Why aren't all research articles on PubMed?
I was recently doing some research on PubMed and I noticed that, in my field of research (plant science), some articles are referenced and others are not, even for two articles in the same journal...
Does everyone know what is (are) the condition(s) for a paper to be listed in PubMed?

Please can you add to the question a bit about the research you've done to answer this yourself, to avoid duplication of effort? And please do add in any relevant information you've found on PubMed help / about / faq ages.

See http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.PubMed_Coverage and http://www.nlm.nih.gov/pubs/factsheets/dif_med_pub.html in particular. But wow, was that buried deep. (Ps. Not posted as an answer because a proper answer really should summarize the pages, not just link to them. If anyone wants to do that, please feel welcome.)

you should write a paper reporting all that :)

Because there are non-biomedical research articles?  Would you really expect to find physics or economics research papers on PubMed?

@JeffE my filed of research is plant science (I updated the original question) why is not in biomedical research. However, many article in plant science ARE referenced on PubMed, while some are not, even on the same topic...

In response to llmari Karonen's comment, I voted to close this question because National Library of Medicine(NLM) would be the only authority to answer this question - they are responsible. Please contact NLM directly.

@scaaahu you could extend that reasoning to all other questions on this site :)

@F'x PubMed comprises over 22 million citations maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).  NLM is the best source of information.

@scaaahu but not the unique source of information.

Because PubMed is about biomedical literature and life science journals. Things are blurry, however, because of two factors:

Obviously, there is no strict definition of what is (or is not) biomedicine.
PubMed does not select “article by article”, but has a list of indexed journals, from which all papers are indexed. Yet, a single journal's scope can be very varied.

Combine the two, and you get the idea that there is a lot of variability in whether an article on a given topic is published. For example, my own research field is materials chemistry, and about two-thirds of my papers appear to be indexed in PubMed: probably because those were published in generic chemistry journals, which also happen to publish some papers of relevant to life science.

from here
The National Library of Medicine uses an NIH-chartered committee, the Literature Selection Technical Review Committee (LSTRC), to review all new biomedical and health journal titles and recommend those to be indexed for MEDLINE®. The NLM Fact Sheet titled "MEDLINE Journal Selection" provides information on the role of the LSTRC and critical factors considered in making the decision to recommend a journal title for indexing. It is intended only as a guide since there is no one set of characteristics that will guarantee selection. The LSTRC considers the quality of the scientific content, including originality, and the importance of the content for the MEDLINE audience throughout the world.

Often there are journals that clearly have bio-medical content, and are not found in PubMed. That's because registering a journal in PubMed is a non-trivial task.
Even for big players like Cell Press it took almost a year to put "Cell Reports"
in there.
The publisher can apply to be included in PubMed, but that usually takes some time. The meeting where it is discussed if a journal is included is only held twice per year. One requirement is that the journal is also available in print. That's why many journals start with a print issue and then after inclusion in PubMed drop it again.

Let me start by saying that some of the other answers are misleading because Medline is not the same as Pubmed. You'll find Medline-indexed journals which are selected by LSTRC in Pubmed, but Pubmed also contains other articles from non-Medline indexed journals - hence the answer about LSTRC selecting Medline journals isn't wrong but does not answer the question at hand.
If a journal is in Pubmed (e.g. because the publisher submits to PubMed Central, or because it is selected for Medline) then usually ALL articles from that journal are in PubMed.
The answer to the mystery why some articles from a journal may be in Pubmed and others are not may have to do with the fact that authors can submit their accepted manuscript to PubMed Central (PMC, which hosts full-text articles) and then they also show up in PubMed. If authors are funded by NIH or other funding agencies they even have a mandate to make their manuscript openly accessible. If the journal is not open access they have to submit it to PMC using the author manuscript submission pathway. The paper will then show up in PubMed, even though the full journal is not Medline indexed.


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Any suggestions to create and maintain a good research atmosphere
I am starting my PhD in Computer Science next semester in a relatively small department (around 20 faculty members). I have been to the university a few times and I noted the collaboration among students is minimal. My prospective supervisor, most likely, is willing to help me in any research activity I propose that will increase the number of projects and publications with collaboration among students.
Thus, I am asking for different suggestions/tips of activities one can do or propose to increase the collaboration and the knowledge exchange among students/faculty members.
My question is on two levels:
1. What activities/set ups can a PhD student do/propose at the group level? (i.e. between you and other students with the same supervisor). FYI, the group is around 10 students. My supervisor is going to set up a group presentation every two weeks.
2. What activities/proposals/set ups can one suggest at the departmental level?  (I was thinking of a weekly talk over coffee for graduate students in the department.)

I seriously hope that biweekly here means “every two weeks”, not “twice a week” :)

@F'x yes every two weeks. thought biweekly is the correct word for it :)

@seteropere biweekly can mean both, hence my question

where are you doing your PhD? Mostly out of curiosity, but also I like to compare and hear about the inter-people lab-dynamics in different cultural environments.

@penelope i'm studying in Canada.

I met a few Canadian scientists-in-making, they all seemed like people that would enjoy a few informal get-togethers during and outside workhours :)

Biweekly usually means every two weeks; semiweekly means every half week (twice a week).

There are so many group-binding activities that you can imagine… I’ll try to list just a few ideas specific to an academic setting:

Journal club, the obvious choice
Friday’s coffee and pastries, or Tuesday’s four o’ clock tea sessions, followed by flash updates (news from the group, recent awards, publications, maybe one existential technical question that someone raises, etc.)
Graduate students seminars: organizing seminars specifically tailored for graduate students (but inviting all those who may want to come, of course). Possible topics include early career path presentation and advice, motivational speakers (e.g. Jorge Cham from PhD comics fame), teaching skills (for TA’s), etc.
Encourage participation in group life: elect students’ representative to lab council or other local boards, hold regular meetings to talk about the practical aspects of your life, organize activities centered around your office space (cleaning day, fire safety day, first responder training).
Participate in competitions in (or near) your field, if there are any (competitions, olympiads, etc.)

All events, even if some seem only remotely relevant to the pursuit of your academic happiness, will increase group cohesion and maintain a good research atmosphere.
For all such events, favour informal settings and try to take as little time as possible. People already have heavy schedules, and they can make room for small activities but probably not a weekly two-hours setting. Brown bag seminar is one way of achieving this.

I just started working in a small lab a few months ago. I don't know if the way our lab is functioning is right or even good, but I like it, it works for me and I feel good here, so let me explain the lab dynamic here.
Just to give some context, the lab is so small that the division to project teams (although it exists) does not make sense for any informal activity. At any given time, there is 7 - 10 PhD students in the lab, maybe 1 or 2 exchange students/interns, and we have some PhD students that are in the lab only a day or two a week. Also, the lab is almost circular, all the offices are very close and we have a habit working with open office doors.
The common topic denominator among all of us is "Computer Science" (very broad), although each of us can find one or two more student-people working a similar topic.
I find that it's much easier for me to talk science to somebody I feel comfortable having a beer and a few laughs with as well. Not saying that you have to get your lab drunk, but:

in the morning, the first one in makes the coffee, and we linger in the lab-kitchen for 20-30 minutes until our eyes are open. Everybody is free to join, heavy coffee drinkers are almost always there, while the others wander in from time to time. Sometimes even the senior researchers have coffee with us.
we all go to lunch together (partially cause we all have partially refunded meals in that resto). We have a guy who talks much and eats slow, so by the time everybody finishes, we usually spend a quality 30-40 minutes talking. We also do a coffee after lunch.
When somebody's leaving the lab, we try to buy some trinkets (last time it was 1euro/person), organize small going away "party" in the lab with juice and cookies, and dinner followed by drinks in the evening. Food setting is more inviting to the shy students, and after that the outgoing ones go have a few pints.
Students sometimes just wander in other student's offices (usually in the lazy afternoon hours) for a few words. This habit is nice because you feel less uneasy when you stroll into somebodies office to talk science, cause you're practically doing the same thing. As a less imposing version, we sometimes just wave to each other while passing in front of the office.
When we have organized (boring) activities / administrative seminars / things that finish early, especially out of the lab, we try to go sit for drinks if we have time.
the only nice idea specifically targeted for professional exchange we did was organize a "PhD students day" where we all presented our subjects in very basic streaks, from 10 - 15 minutes, so that everybody would know which students are working on interesting problems (for them).
every project team has team meetings at their own pace, where we present our current research, recently accepted papers, exchange students present their topics or students that went to an exchange present what they did. My team does it usually two times a month, in a fairly casual setting.

Now that I mentioned all this procrastinating, let me say something that's always been true for me among Computer Science people wherever I went (studied in Croatia, Austria and now France, and had some holidays with CS people): you can't stop computer scientists talking about tech. Tech talk bleeds through beer, we eat some of it for lunch and drink it in our coffee. When we're happy about our work, we feel comfortable enough to share it with people around us. When we're angry and stuck, we are all around people who saw us in various kinds of settings, so we don't feel that uncomfortable being grumpy and complaining.
All this said, for some more context: I'm a PhD student in France. I have a feeling that the work environment here is much much more relaxed that in the States, and than a lot of European countries as well. They seem to believe that if you do everything slowly and relaxed (except a day before a deadline), you will do a good job. So, my advice might be only applicable to similar work cultures, but I still think there's some good things there, because, at the end of the day, we all enjoy our times in the lab.

+1 for "all this procrastinating", which it really isn't.

I'd like to add that "organized" informal meetings (coffee, lunch) are IMHO generally important. Including informal gatherings where the supervisors/directors/professors and also the technicians come. It's the thing to attend if you want to know what is going on. And you can discuss/solve/do lots of these these tiny little points (supervisors!) that should be said but about which you'd never actively want to disturb someone.

I'm not sure I should be contributing to a list like this, but other people seem to think it's okay, so... in addition to what has been suggested in other answers, one thing that I've found quite useful is to have a small research discussion group among the PhD students.
The way this works is that you get about 10-15 students together from different fields within the department, to meet every week or every other week for an hour or less. At each meeting, one of the group will talk about his or her recent research. These talks are normally "beyond informal" in the sense that no prior preparation at all is expected; effectively, you're just explaining what you do to your friends. It works best when the "audience" members feel free to ask any stupid questions that may occur to them, which means two things: it's ideal if the people meeting already know each other in a non-academic context, and also important to do it without faculty involvement so that nobody is tempted to try to impress a professor. Having students from a variety of different fields of research means that you can expect to have some pretty basic questions at each presentation.

It's a nice contribution, why do you think you shouldn't try to contribute? :confused: isn't contributing the whole point??

It's because this seems like a list question.

Academia.SE has more relaxed limits for what is subjective and what is list-based, compared to more fact-based sites like Physics…

A few more points:

as undergrad students, we had a campfire to celebrate the end of labwork/seminars/lectures.
now (on the teaching side) we have a campfire to celebrate the end of labwork/seminar/lectures.
(it usually includes some birthdays as well)
in one institute we had quite regularly after-work activities like a bike tour, going swimming, bowling, Xmas market etc. happened. They were "scheduled" every once in a while, so no problem if you'd like to come in general, but just not that day. You could just join in next time (however, next morning at coffee you'd of course hear what you did miss). This included everyone in the institute but the big boss.
(Sometimes people signed up for university sports courses together.)

We did regular "happy hours" about once a week - going out for drinks or to somebody's place for some activity (or once in two weeks if there were deadlines) with my last team, which doubled as in-team birthdays and other celebrations. People would also bring something sweet to eat at morning coffee. But, I contained my answer to my current environment, which is a bit different (also a bit more international) than the one I with during my internship.

I am part of an  interdisciplinary NSF IGERT program on Water Diplomacy which supports 15 or so PhD students across 4+ departments. The program has done a commendable job of making opportunities for team building, collaboration, and the emergence of happy accidents within the group. Here are a few things to add to the running list of answers:

Weekly colloquiums where one student presents their work for an hour, followed by half an hour of collective brainstorming, critique, and discussion. Light breakfast provided.
Annual weekend retreats to revisit program priorities, assets, and areas for improvement. We cook meals, have fires, and chat.
Monthly evening workshops/round-table discussions on a theme - this year's series is on civic engagement. Dinner provided.
Share office space. While not uncommon for PhD research groups, it's unique to have students across multiple departments sharing space.


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How should we sort the names of the authors of a paper (with two authors) when they have the same contribution?
Me and one of my friends have recently written a paper and we have almost the same contribution. Is there any conventional way to express this and show this ?
How do we sort the name of the authors in such a case?

There is a precedent of using a series of croquet games to determine the first author. Or you could just agree to alternate, and make sure you collaborate on an even number of papers.

@UV-D source - the delightful "scientific papers easter eggs" tumblr

The most common is to list in alphabetical order (in fact you can decide whatever you want) and then write a statement in the acknowledgement to the effect that "both authors have contributed equally to the paper".
In one (odd) example I know of names were listed in reverse alphabetical order. The "first author" was the senior and the second his (in this case) graduate student. They then stated in the acknowledgement that contributions were equal. So in this case the senior scientist wanted the publication listed under his name although it would have been more logical with the students name first. So it is obvious there may be several "reasons" to list other than alphabetical but I think alphabetical should be the way to go. At least in my subject order typically signifies contribution and an inverse order would be a very strong signal.
I have also seen authors who have taken turns to be first when they frequently publish together. That could be a reasonable (fair) alternative when it happens.

The "first author" was the senior and the second his (in this case) graduate student. They then stated in the acknowledgement that contributions were equal. — That's just mean.

I agree with the point of taking turns to write the author sequence. It greatly encourages to work in collaboration which is the most important goal of research and publications.


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Include Shortlisted Awards?
At undergrad level I was short-listed for the most prestigious award at my university (best graduate of that year). I however did not receive it. I did not get any paper or other evidence stating that I was short-listed. I only know this because my personal tutor told me. She also mentions it in her reference letter for me. Should I include this in my CV? Such as: Shortlisted for award X?

Anyway, if it is cited in a reference letter, do you really need to list it on a CV?

She simply mentions the name and not what the award is actually for. In my CV I have one line explaining what the award is for.

Do you think I should email the University and ask for some letter to confirm that I was short-listed? This has been over a year though.

I will contradict Peter's answer: the CV is a living document, but it's one that needs to be supported by documentation. Something that cannot be proven should not be listed on a CV. If you only received a verbal confirmation that you were on the "short list" for an award, then you really don't have any documentation that you can provide, if called on to do so by a future employer.
Therefore, as much as it would be helpful to list such an award, I don't think it's a good idea to do so here.

My personal tutor however mentions it in her reference letter. Would that not be enough to verify it?

No. CV should be verifiable independently of other things. Besides, it is hard to compare "being shortlisted" to achievements of other people. We all understand already that "the best" at some locality may mean anything from "a superstar" to "not so bad compared to the general background", so even the actual prize may not be revered unless your university is very well known. Anything below it is just too vague and immediately raises the questions like "How short was the list?", "How strong were other contestants?", "How many orders of magnitude better was the actual winner?", etc.

@fedja unless you have the numbers added to the CV! For example see my answer below. In that case it says "3 finalists from 29 nominations out of 349 eligible staff" and this info is verifiable because it is in an email directly from the official university email account responsible for administering the award.

While aeismail and Peter's answers are both quite good, it strikes me as a very complicated issue. It does seem that you have some documentation that you got it and I agree with Peter that earlier in your career your CV can look quite empty so having anything to put on it can help show yourself in a better light.
On one hand, someone nominated for an academy award would certainly be referred to as 'Oscar Nominated.' On the other hand, to say you were short-listed for an award such as this (since from the title it is not clear how students are compared to each other) may come across as trying too hard.
I do think it would be acceptable and that you have some (albeit weak) evidence. However, were I in your shoes, I would not include it out of concern of looking too desperate to find good things to say about myself.

The "documentation" is a mention in a letter of reference. That's not quite the same thing as a letter from the committee making the decision!

@aeismail Yes, I agree. That's why I said it was weak evidence. It's not nothing...but it is not great evidence.

Besides, as a general practice, you aren't assumed to know what is written in your reference letters, so to put it on the table won't be easy...

While I totally agree with this, I've seen a lot of "trying too hard" CVs and it's hard to fault the students, since we're demanding they compete with a (expectedly) rather barren set of accomplishments. Then again, if I got the CV of an award-runner-up, I'd probably look up the winner and invite him or her to apply. ;)

A CV is a living document that changes over time. early in one's career, there is not much one can put into it but hopefully this changes over time. I argue that one can put anything into a CV which strengthens ones profile at the stage at which one is at the moment. In other words, it sounds perfectly in line to add your short-listing now. At some point later such an item will probably not be worth keeping but that is a judgement call to be made depending on where you are in your career and what else is in the CV. Another factor to keep in mind is that CV content will vary depending on for what you need it.
So if you think something will positively reflect on your capacity in the light of for what you need the CV, add it!

Yes you can, but you need to put contextual information next to the nomination. Writing the contextual information will help you decide whether being nominated for the award is an impressive achievement, and whether it is relevant to whatever you are applying for. For example I was a finalist for a "Faculty of Science Award" at my school for research excellence [I'm a postdoc]. I initially thought I wouldn't put it on my CV, because I didn't win. But then I had the idea to email the faculty of science to ask how many academic staff were eligible for the award and how many nominations they received, after hearing the answer I decided to add it to my CV. I now say

Finalist for X Award [3 finalists selected from 29 nominations, out of 349 eligible academic staff]

However, if they told me only 5 people were nominated and there were only 20 eligible people who could have potentially received the award. I wouldn't have added it. If you can't briefly explain the nomination in an impressive way using verifiable facts then don't include it [note that the email directly from the head of Faculty of Science makes the facts verifiable if anyone asks for proof].


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Visiting Student/Scholar

Can one be titled "Vising Student/Scholar" at a university if one is already graduated from another institute (with BSc/MSc) and is currently not affiliated with any university?
Does one have to pay registration fees, etc.?
In this case, can one be paid for as a TA/RA by the university?

Is it different in US and EU?

I suppose it depends on the exact nature of the position, and each university has different rules. At least in EU, that's the case. “Visiting student” or “visiting scholar” is just a generic term covering many different realities…

This answer is based on my experience in the US.  It won't necessarily apply to every institution.
Typically, these titles are used for people visiting University X for an extended period (one or more academic terms) to work on a research project with a faculty member (call her Prof. A) who is already there.  If this is not your situation, then please clarify your question.
You would not be employed by University X, but would typically be entitled to courtesies such as library privileges, computer access, and perhaps office space.  The exact qualifications needed for each title may vary, but if Prof. A wants you to visit, she can probably arrange for you to get whichever one is appropriate for you.
I would expect that if you are not attending classes, you wouldn't pay tuition or fees.  There might be a nominal fee for a library card or something like that.
Teaching assistantships would generally be reserved for University X's own enrolled (degree-seeking) students.  It is conceivable that you might be able to get one if they are really short staffed, but probably unlikely.
If you want to get paid for teaching, depending on University X's policies and needs, you might be able to get an appointment as an adjunct professor or instructor.  This would be something for Prof. A to bring up with her department chair.  At some places an MSc would be sufficient for such an appointment, but other universities might require a PhD.
The most likely way to get a research assistantship would be from Prof. A's grant funding.  It would depend on the specifics of her grant, the rules of the funding agency, and the rules of University X.  In any case, her own official graduate students would probably have priority.  Again, this might depend on how strongly she wants you to visit.

You are right, I meant to work with a faculty member. So my understanding is that I do not need to be a student at somewhere else before becoming a visiting at a new place. Thanks for your answer.

It's too broad a statement to say that this is valid throughout the US. With 3,000 colleges and universities, each with their own system, it's difficult to say "you won't be charged fees," or how things work in general.

@aeismail: Thanks.  I edited to equivocate further.

I think that there are a lot of different variations, between continents, countries, and even individual universities. It is definitely true that pretty much every school in the US will have its own policy (since there are no national policies regarding registration in the US—although there are some rules that apply to financial aid obtained from federal sources). In Europe, things can also vary greatly between countries and schools (although they're trying to standardize things, this is still very much a work in progress).
Your best bet is to contact officials at the international office of whatever institutions you're interested in attending, and asking them directly.

Contacting the international office is also a good idea. Thanks.


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How formal should figures in a thesis be?
I am currently writing my masters thesis. I include in it a screenshot of a webpage, in which I want to point at some components and explain what each of them does. What I did so far is that I draw circles around the components and an arrow from the component to a one word text saying what it is, I intend to go into details under the image.
Is that sort of “labeling” formal enough for a thesis figure? Or is there another presentation that would be more appropriate?

-1: I don't think that the purpose of Academia.SE is to give advice on how to present a document.

Images in a thesis should be of the same quality as images in a peer-reviewed publication. Hand drawn circles and arrows are not formal enough. Circles and arrows drawn with programs like TeX, GIMP, Illustrator, or Powerpoint are formal enough.

I agree.  The whole point of thesis documents (or dissertations) is to be formal.


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Citing books in scientific articles
I'm writing an article that has something to do with the multipole expansion with irreducible tensor operators. The topic is old, and I only find books talking about it.
So is it OK to cite tertiary sources (books) in scientific journals? or must it be a primary source source article? Or does it depend on the journal?
The question I'm asking is general about citation rules, and not for this specific case, though this specific case with irreducible tensor operators is what I'm facing right now.

I don't think there is a problem with citing books. I assume the book in question does not cite an original source itself. I don't think spending a lot of energy looking for a primary source is useful.

Yes, citing books is fine (including anything from research monographs to elementary textbooks).  The question you should ask yourself is what the citation is for.  What are you trying to convey to the reader?  For example, if you are trying to assign intellectual credit, then you should cite whoever originally made the discovery.  However, that's far from the only reason to give a citation.  If you are providing references to background or more detailed explanations, then all you need is a source that explains what you need, and sometimes a textbook will be clearer or more useful than a research paper.  If you are supplying a citation to back up a potentially controversial claim, then you need an authoritative source.
The specific topic you mention is mathematical, in which case the distinction between primary, secondary, and tertiary sources is not particularly important except for assigning credit.  As far as explanations go, any derivation will do.  Of course, the form of your citation should indicate your intention.  For example, if you cite a textbook, you can say something like "See [insert reference] for an exposition of the theory of irreducible tensor operators" to make sure it doesn't look like you are claiming this book is where the theory originated.
Of course other fields may attach far more weight to these distinctions.

@user8458 References should also be as specific as possible, which usually means providing page numbers. Unless the whole book is about the topic you're refering to it for, you need page numbers.


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How to cite a rebuilt graphic
I'm going to have my first presentation in some weeks. Therefore I read some papers and now I'm building the presentation with LaTeX.
In the papers, I found some very useful graphics. But for quality reasons I don't like to take Screenshots of the PDF's. So I rebuild the graphics to have them as vector graphics.
Can I cite them just like I took a screenshot, or is there a difference?

Some PDF viewers (for example, Perview and Skim on the Mac) allow you to extract portions of a PDF file in native PDF format, which avoids the aliasing issues of "screenshots".

Rebuild from...? (I.e. from raw data, from reverse-engineered plot, or just vectorization of the graphics?)

@PiotrMigdal I think rebuild may be the wrong word. Reconstruct would be more apposite. I used TikZ and made my graphic look very similar to the one from the paper.

There are two parts to this question: citation and copyright issues.

Regarding citation: cite the source of the data/graphics/charts/schemes.
For the copyright part, if the presentation of the data is really identical, most journals liberally give permission for reüse (you have to ask for it), but require an acknowledgement of the form “Reprinted with permission from …”. That should cover modifications in format (bitmap to vectorial, or bitmap downsampling, etc.), but I have already seen people actually note the difference by using “Redrawn with permission from …”. Now, if the figure is based on the first one, but with substantial modifications, you can be happy with only citing the source, or possibly adding “Figure based on X with permission from …”.

If Dave's presentation is only for an academic purpose i.e. A lab seminar, is this still necessary, Dave did not mention it though, and I wholeheartedly agree that proper citation and permissions are due for a conference presentation.

@Leonpalafox Citation is clear, but is permission really required for a conference presentation? I always thought it would fall under fair use. One or two figures from a paper is a small part, and you can probably argue that you are using it for review / critique of the original source.

@silvado the first rule of fair use is: “unless you are a lawyer, don't talk about fair use”… (it's really tricky)

@F'x (When it comes to the second point.) Seriously? For reusing plots in papers, anything publishable, or a more serious website - sure. But for using such for slides, I never ask (and never will :)), as probably vast majority of others. It's not as if I were taking advantage of their effort - I'm promoting their work!

@F'x (except, maybe, for journal-made plots)

@PiotrMigdal I am not saying it is not fair use, only that it is a complex and somewhat gray area. Also, I am not saying that it is morally wrong, either. Actually, I do the same as you: I only request permission for figures I publish in books and papers, not conference slides. But I don't think the legality of this is a settled matter.

@F'x Sure, I'm aware that it is legally a gray area (and, very likely, depend on country; very likely in some you can cite (i.e quote) a small part of any material). However, as it is not a legal question, but "what to do" - IMHO it's the best to refer to actual practice.

@F'x thanks for the answer. I'm sorry that it took me some days to respond. As Leon palafox suspected it is only for academic purpose. But I thought about the question it did not came to an answer.

For presentations, when you are using graphics from other papers, you refer to the paper. The most important think is not to pretend that it's yours and to point to the source (perhaps your whole point of this slide is to refer to a specific paper).
You may add "from [cite]" but usually it's "obvious".
Also, if the graphical differences are not trivial (i.e. programs almost always modify graphics anyway), you can add something like "redrawn from data from [cite]".


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May authors opt-out of the proceedings of a conference?
Many conferences in my field (theoretical CS) are organised as follows. They are run by academics, as an endowement, scientific association, or some other not-for-profit organization. Each year, submission and reviewing are done on some platform like Easychair, producing a list of accepted papers. The authors of these papers are then requested to submit a final version of their work (or camera-ready) for inclusion in the proceedings of the conference. The proceedings are managed by a for-profit scientific publisher (e.g., Springer, Sheridan Communications, etc.), and the authors are asked to sign a copyright transfer agreement, so that the publisher can sell the final version on their website. The publisher may edit the final version, but in most cases it doesn't: the publisher's only role in the conference is apparently to compile these proceedings.
To make papers more broadly available, it seems to me that authors could prefer to simply host the final version of their work on an open repository like arXiv, as they often do anyway, instead of publishing their work in the conference proceedings. (Alternatively, they could simply submit the title and abstract to the publisher, along with a pointer to the arXiv version.) This would save authors the effort of dealing with the publisher's formatting requirement, and would also avoid any potential legal issues with the copyright transfer (which do not always allow authors to host their work elsewhere). Further, it seems to me that it would make no difference to all the rest of the conference organization.
Hence my question: Are some conferences OK with authors hosting their work somewhere else than in the publisher-run proceedings? More generally, do conferences care whether the authors of an accepted paper actually submit a camera-ready version to the publisher? If yes, why, and what happens when authors fail to obey? If no, why do authors bother?
(I imagine that authors may want to include the accepted paper to their résumé, but instead of listing their paper as being "published in the Proceedings of XYZ", they could point to the arXiv version with a note "Accepted/presented at the XYZ conference": presumably, this should make no difference?)
(Related: this question suggest that some conferences allow what I propose (for different reasons, apparently), but I have never heard about such conferences in my subfield. Why aren't there more of them?)

I am not sure about the point of your question. One submits a paper to a conference to be included in the conference proceedings. If you do not want to be included in the proceedings, it makes no sense to submit to a conference. Also this "This would save authors the effort of dealing with the publisher's formatting requirement" is wrong, because (in most cases) when you submit a paper at a conference (through e.g. easy chair), you are supposed to follow the proceedings format. So, there are no extra formatting required for the camera ready version...

...Also, e.g., Springer allows the post-review manuscript to be uploaded on Arxiv or your personal web page. Why would not anybody want to also include the paper on the proceedings as well? DBLP for example indexes arxiv as unofficial publications, whereas proceedings are indexed as conference and workshop papers.

@Alexandros: Thanks for your comments! About formatting, for many conferences in my field, the conference's formatting requirement are different from the publisher's requirement (in terms of font, number of pages...). In terms of rights, many publishers do not allow authors, e.g., to publish my work under an open license anywhere I like (so that anyone can redistribute it). As for the point of the question, for me the main point of submitting your work to a conference is to present the work at the conference, not getting it included in the proceedings, no?

"for me the main point of submitting your work to a conference is to present the work at the conference". If the conference is good, you also need proof that your work was indeed presented in this conference and this is exactly what conference proceedings are for. Without proceedings how can you prove that your work was presented there and how would e.g. DBLP will index your work as presented in this conference?

Many conferences publish lists of accepted papers besides the proceedings. (e.g., in my field, databases, they are usually mailed out on the DBWORLD list), in addition to the schedules. But alternatively, you could just put the title and abstract and pointer to the full version in the conference proceedings: this gives you a tangible proof, while leaving you free to host the full version elsewhere. (But I'm not sure why you would need a proof, actually. If you say that your work was accepted at conf XYZ, who would doubt it? Who would be so foolish so as to fabricate such a claim?)

I don't know if there would be any negative consequences from the conference from refusing to include your paper in the proceedings, but there are several positive reasons to do so. I don't know about theoretical CS, but I understand that for many sub-disciplines of CS, the conference publication is more imporant for your career than any journal publication. So, if yours in one where the conference article is more important than the journal article, you may have already accomplished the most important part for you already by the time you give the talk. That being said however, you might still prefer to put the paper into the proceedings volume since:

it should be easier to find and refer to for future researchers and yourself than if it is on your website or the arXiv
a journal special issue is probably considered more archival than arXiv.org by some
if your discipline is other than I mentioned, you now might be considered to have a more prestigious journal article as well (depending, often, on whether others understand the level of peer review associated with that conference).

If this printing is a free service of the conference and goes in the publisher's digital archive, I'd be inclined to take the opportunity over trying to host it myself or arXiv it, and I have done so, even though CS is not my primary discipline. I'm not a big fan of the copyright transfer that is basically required to allow the big publisher or the professional societies to publish a copy of your work that they did not author (at least in the US and Europe).
I'd say that it's unlikely to be a big problem with the conference for you not to publish in the proceedings, though you might get some pressure from them to include your article. Some of the organizers, if they are common one year to the next, might remember your refusal and hold that against you the next year, but that would be unethical in my view, so they might also just let it go. As long as the paperwork to submit the article to the proceedings comes after the conference, there's not much they can do to you before the conference (like pull your talk), so I wouldn't worry too much about that. Finally, before you sign the copyright transfer with the publisher, you have an opportunity to read the publishing agreement and decide if it currently or ever will meet your standards for openness. If it doesn't or never will, then you can make that call as late as possible if you want to.

Thanks for your answer! I am unsure about what you call the "journal article". In CS, as far as I know, conferences have proceedings, not journals, and submitting to a journal is an entirely separate process. Usually, publishing your work in the conference proceedings does not prevent you from publishing an expanded version to a journal later. So I wasn't talking about whether the conference work could be also submitted to a journal or not.

In terms of pressure, conferences in my field usually arrange the proceedings and copyright transfer before the conference takes place, so it would be technically possible for them to pull a talk if the work is not submitted to the proceedings. But I still don't understand: why would they mind? I have a vague feeling that they might, but I do not really understand why.

@a3nm, a) if you look around, there are theoretical CS journals that are separate from conferences, b) it's a package deal. If the conference expects you to put your paper in the proceedings, they might be offended by your snub of the proceedings volume since they put the time and effort into reviewing your article. That might lead them to pulling it. There might be an implicit or explicit agreement that if your article is accepted, you will agree to the publication in the proceedings.

Look at the call for papers carefully. You generally have already agreed to show up and present, so the later publication might also be in the submission rules. Also, you might have only signed a copyright transfer to the conference not the publisher that allows them some rights for publishing an abstract or other summary of your paper. Look even more carefully at that before you sign it.

I think this depends very much on the culture of your field.
I'm in a field (bio-/medical optical spectroscopy; chemistry) where conference proceedings count much less than "proper journal articles" (and they are subject to muss less strict reviewing). Consequently, we don't have much proceedings volumes (some conferences try to enforce submission of a proceedings paper if they have). I think this is because conferences are often comparably small and consequently try to get as many participants as possible. However, travel funding is usually tied to presenting at the conference. Thus, almost all participants typically present either a talk or at least a poster. The review process decides who gets an oral presentation (unless you opt out and immediately say you'd like to have a poster) rather than who presents and who should not present at all.
Instead, there often is a special issue in one of the normal journals where the paper is subject to the normal peer-review process. These themed issues are more or less tightly bound to the conference (we once were asked whether we'd want out paper to be put into one such issue. The paper wasn't presented at the conference, but it would have been on topic).
Also, it is quite common to present preliminary results at the conference. As it may take more time to finish and write up the study, it is quite normal to submit the manuscript to a suitable (other) journal when it is ready.
To give an example with numbers: Spec 2014 had 62 oral + 191 poster presentations with 282 participants. The Analyst themed collection has 53 full papers + 3 communication papers.
arXiv counts even less as there is no peer review. arXiv is considered only for depositing a manuscript in addition to the publication in a peer-reviewed journal. Fortunately, most publishers nowadays allow arXiv, and even if they don't in my country (Germany) the copyright law now has a clause that allows to make the manuscript publicly available after some embargo period.


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When moving from one institution to another, at what point should I change the affiliation on the papers?
When publishing a paper, I normally go through the following stages (which I imagine are fairly universal):

Figuring out the solution to a new problem and writing it down.

Polishing up the manuscript until all of the coauthors are happy.

Putting the preprint on arXiv and any number of other repositories.

Submitting the paper to a journal (or several journals, if the first one rejects).

Revising the paper until the referee is happy, and getting it published.

Suppose that at some point in this process I move from University A to University B. When is the exact point where I should change the affiliation listed on the paper from A to B? This type of question has come up several times for me, but luckily in all cases I was either fairly early or fairly late in the process and the answer was clear enough. Still, I feel like I should have a clear idea of when the transition happens, and, much to my embarassment, I don't.
(If it matters, the field is pure mathematics.)

Number 3 and 4 are both points on the time line (whereas the others are time periods) so I would use the current affiliation at that point in time for both of these.
If you affiliation changes during stage 1 or 2 I would usually put the final affiliation in the paper. An exception might be if the first affiliation is through a grant and the paper is essentially what the grant paid for.

Affiliation serves (at least) two purposes: to give credit to institutions that support you in the research and to enable readers to find you.
Some institutions are also possibly sensitive about affiliation and, if you leave, don't consider you affiliated with them any more.
With this in mind, I find a general, one size fits all, solution impossible.
My own preference, provided that other concerned parties don't disagree, is to list my current affiliation, but note in the paper when and if the research was carried out at another institution, even if only in part.
It is also useful, since affiliation statements usually include an email address, that you provide one that will be honored into the future. My own former employer (retired more than a decade ago) has been good enough to keep me in the email system.
I'm trained as a mathematician but have published mostly in CS where my "preference" seems to work. It might be different in a lab science (chemistry, physics, biology,...) where the support is much deeper and more explicit.

Check the journal guidelines to see whether they say anything about this. I have certainly seen journals that say affiliation should reflect where the bulk of the work (by which I assume they mean your stage 1) was done, journals that say the affiliation should be your current institution, and cases where I couldn't find any specific guidance.
Unless the journal says something to the contrary, I would update my affiliation to be current every time a new version is produced, i.e. at point 3, point 4 (every time), and at each revision during 5. (I wouldn't attempt to make changes later than this, such as at proofing, and I wouldn't make pre-emptive changes based on upcoming moves.)
Some people give a fuller explanation by listing their affiliation as something like "University B (research conducted while at University A)".


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Is it good practice to have hyperlinks in bibliographies?
Lately I have been thinking about what is the right way to cite other papers (i.e., what to put in the bibliography entries, in the section which is typically called "References"). As many papers are available online nowadays, it seems to me that bibliographic references should include, whenever possible, a link to the paper being cited: this is supported by the PDF format, and is easy to do (at least for works typeset in LaTeX: e.g., with \href{} or \url{}). Yet, strangely, I have never seen a paper whose bibliography entries consistently featured URLs or hyperlinks to the works being cited. Is it good practice to include hyperlinks in bibliographies? If yes, why is essentially no one doing it?
One possible explanation is laziness on the part of the authors, but, strangely, there are still many papers whose bibliography entries include information about volumes, series, and page numbers, even though in my field (computer science) I have never seen anyone look up a paper using this information: people just search for papers with Google using the title and authors every time (in other words, they work around the non-existence of a hyperlink which should be there). Maybe the explanation is that existing bibliography management tools make it easier to manage page information than URLs? But is this just inertia, or is there a good reason?
A side question is assuming you want to have hyperlinks in your bibliography, which hyperlinks should you use? I have a preference to link to open-access versions of the cited papers (i.e., which aren't paywalled, so everyone can follow the link), but this sometimes conflicts with other desiderata, such as having a stable URL (e.g., not a PDF on some author's personal web site), having a link which indicates the DOI of the paper, etc. Which criteria should one preferably follow?
Another side question in this case is how should the links be formatted? One possibility is to write out the URLs explicitly, but this ends up taking a lot of space, and may be illegible, especially for long URLs. The other option is to use \href{}, i.e., put a hyperlink on the paper title, but this is probably not very discoverable, and it means information is lost whenever someone prints the paper. Which one is preferable, or are there other formatting options?
Edit: For papers submitted to publishers, indeed, it probably suffices to follow the publisher style (although the question remains of why so little publishers seem to be doing it). My question was more about preprints and author-final versions, prepared by the authors to be published online (e.g., on arXiv) independently from any specific publisher.
Related questions (with URLs ;)):

Should I include a DOI/website URL for a publication in dissertation bibliography?
Publishing DOIs instead of traditional references?
What are the downsides of using DOIs in reference sections of publications?

I've seen quite a few recent papers which cite preprints using the relevant arXiv identification number. Using this means the information won't be lost if the paper is printed. However, when citing a published paper it seems that the full citation is expected. Perhaps this is field dependent (I'm in theoretical physics)?

For me it sounds like a cool idea. It could be the DOI as a link, which eventually could direct to the original paper regardless if its link has changed. But I think it is sometimes done from the publisher's side (as often there are links using Crossref) and don't rely on the authors to provide the respective information. Actually, I remember that during production, sometimes they cannot find some references, so they definitely (at least some of the publishers) look for the actual reference papers and probably at the same time collect the information to link to them.

@BioGeo: The problem of linking to DOIs is that they tend to redirect to paywalled versions of the articles on publisher webpages, so there are many readers who cannot follow such links. One possibility is to use doai.io or oadoi.org, but I don't know whether this is the best option (also they can't always find the preprints when they exist).

@a3nm I suspect that any other link (directing to the "free" version of an article) than DOI would be illegal, so I'm not sure any journal would prefer the options you mention (which I admit I hadn't heard) over the "real" one.

@BioGeo: Free versions of an article are generally not illegal. Many publishers allow authors to put free preprints online on repositories like arXiv, institutional repositories, and personal home pages. (See e.g. http://academia.stackexchange.com/q/72809). In fact I wasn't thinking about putting links to free copies of articles without a clear legal status, e.g., Sci-Hub; I was mostly thinking about legal preprints on arXiv and elsewhere.

@a3nm: Unlike the DOI links, though, such links can be highly unstable. In any case, when I click a DOI, I would normally expect to be taken nowhere else but somewhere that actually resolves the DOI.

@O.R.Mapper: Yes, links to personal webpages can be unstable, but some others aren't (e.g., the links to arXiv). About the semantics of DOI, I agree with you to some extent, but when clicking a link to a paper I mostly expect to be taken to the paper, not to a paywall trying to change me to obtain the paper. So maybe DOI links are not the best practice then... or maybe putting them in addition to a usable URL...

@a3nm I understand your point and I would definitely prefer to be sent to the free (legal) version of a paper, which could be an arXiv preprint or a research gate personal copy. But still I suspect that Elsevier would not "allow" the link of a reference in their online version to lead to the free copy of it, rather than theirs (or other publishers') official (and often paywall) version.

Ah, I just read your edit on the question! It changes a lot (to my understanding of the issue)! In that case I agree that any free version (even if the website hosting it might become eventually obsolete) might be better than nothing (or than the paywall version). But indeed, most of the references I use are either OA or provided by my library (paying the paywall), so either easily available through the DOI or probably very hard (or too much work) to find a free version without a paywall, respectively.

Maybe I'm a bit late here, but I do think it is among the best practices there can be. I also can't understand why journals' names are abbreviated. IMO providing links is really important for many reasons:

It provides quick access to the cited material (either text or anything else).
If a link is available, checking that source is (normally literally) one click away.
If it isn't, it can be a challenge to get it. If the link is a DOI or other persistent link, it ensures access even if the final link changes. If the link is not persistent, it provides some transparency: the material was online at URL "x" at day "y", so if it's gone it's not your fault but you stated every information you had, and your reader now has some more info to work with when trying to reach that same source (looking for cached/archived versions, maybe looking for other people referencing the same URL who might quote some bigger part or even have an offline copy, who knows...).
A reason for deliberately using a not-DOI URL: "People click on URLs that they understand and view as authoritative", so depending on the domain or subdomain of your cited material's URL, it could be a (not so) subtle persuasive use of that information in one's favor (either a publisher's, a government's, an international body's or any other institution's domain).

And these are just the ones that immediately come to mind now. But I think all the reasons that justify all the efforts to create the idea of DOI as a persistent link and maintain a whole infrastructure around it apply here as reasons to use it.
Actually, the real question could be why not use them (DOIs first, but links in general), and there are as many reasons for not using it as there are for abbreviating journals' names these days.
As to formatting, reason 1 above suggests not using "doi:10.1234/abcd1234" as this is not clickable (unless you manually make each one clickable by formatting it as link etc.), but rather something (automatically) clickable like "https://doi.org/10.1234/abcd1234".
And providing the last date you had successful access to it is useful as well, for what I mentioned in reason 3 above. (Some styles suggest stating the date of your first access. I can't quite see why would this be more important.)

Journal's name are often abbreviated in my field because there is often a page limit on papers which includes the bibliography, so saving space in the bibliography is important...

@a3nm if there's a page limit, then saving a few lines matter, sure. But in digital times like these, why are there such page limits? And even if there are good reasons for page limits (and I agree there might really be), why not set the limit considering fully readable references (i.e., why allow this kind of abbreviation that simply prevent immediate human readability of the references, and BTW humans are the targets here)? It shouldn't increase the total in more than 1 or 2 pages.

ASR: I was just describing the (broken) status quo. I completely agree that it makes no sense for page limits to apply to references,

Yet, strangely, I have never seen a paper whose bibliography entries consistently featured URLs or hyperlinks to the works being cited.

Actually, there are some publishers which consistently report URLs and hyperlinks in the bibliography entries. An example is IOP, and here is an example paper  where hyperlinks are used consistently in the bibliography. Note that, in my experience with this publisher, it's the copy editor who provides most of the links (e.g., DOIs), not the author.

One possible explanation is laziness on the part of the authors

Not necessarily, it can also depend on the publisher's style. For instance, IEEE usually doesn't put hyperlinks to journal papers (for the journals I know of), and I suspect that they would be probably removed if put by an author.

I have never seen anyone look up a paper using this information

Many publishers have search bars where you can enter just journal, volume and first page of the article. I frequently lookup papers in this way, and I know other people who do it.

assuming you want to have hyperlinks in your bibliography, which hyperlinks should you use?

Assuming you want to have hyperlinks in your bibliography, check first the publisher's guidelines: they might not be allowed or the required type might not coincide with your favourite choice. If I were to choose, I would use DOIs for journal papers to have a permanent address to the, possibly, most up to date version of the paper.

how should the links be formatted?

This, again, is usually decided by the publisher. In the IOP example above, most of the links are formatted as coloured hyperreferences by publisher's choice: this is probably the least invasive way, but it might not be supported by other publishers.

Thanks for your answer! However, as I should probably have clarified, my question was about what should be done about the author when they have the choice (e.g., a preprint posted on arXiv or on a personal webpage), not about a camera-ready version submitted to a publisher (for which indeed the publisher style guideline probably applies). Thanks for not making this clear; I edited the question accordingly.

@a3nm Tomorrow I'll add something to address the edited question. Note, however, that if you aren't submitting to a journal, you can even put multiple links, e.g., doi + arXiv link.

Yes, on arXiv I have complete freedom to link to what I like. I'm just wondering what would be the right links to add, and whether it's a good idea (and why aren't more people doing it). Thanks!

One possible explanation is laziness on the part of the authors

Another is laziness on the part of the publishers. I normally get my Bibtex entries from Mathscinet, and they include url and doi fields. Yet, in my experience, they rarely get displayed in the final version of my papers. Most journal styles simply ignore them.

OP asks:
assuming you want to have hyperlinks in your bibliography, which hyperlinks should you use? I have a preference to link to open-access versions of the cited papers (i.e., which aren't paywalled, so everyone can follow the link), but this sometimes conflicts with other desiderata, such as having a stable URL (e.g., not a PDF on some author's personal web site), having a link which indicates the DOI of the paper, etc. Which criteria should one preferably follow?

Regarding stable URLs: a PDF on some author's personal web site can be made into a stable URL. Save it to the Wayback Machine . Although it makes the URL part of the bibliography longer, I'd then cite both the original URL, and the Wayback version. The second provides stability; the first, when it still exists, is faster to load, isn't decorated with Wayback Machine headers, and may get updated. I do this with popular writing such as blog posts too: dead links are such a problem.

https://perma.cc/ is what you're supposed to use to produce a citable permalink out of a non-permanent URL. Academic publications ought to be on some open repository with a permalink and a digital preservation plan.

Didn't know about perma.cc . Since the Wayback Machine has been around for a long time, why was perma.cc created? Do its implementors think it will survive longer?

There is no competition between the two: perma.cc is a service by the Internet Archive and others which is meant to perform specialised archivals, just like many national libraries in the world archive the web with Internet Archive's software. It's a way to have more copies across more institutions. https://perma.cc/docs Also, because there is a specific (and tracked) use for the snapshot, the fair use defense against any copyright claim is very strong. And the URLs are shorter!


text:
Examples of a large-scale physics syllabus review
My Department – Physics – is preparing to modernise its entire syllabus at all levels, from undergraduate through to graduate courses. We are looking at what material should be taught, as well as methods for teaching that material. This will be a significant, multi-year project.
I have found plenty of accounts of how others have changed a single course, or a few courses. However I’ve not come across an account of a department changing its whole programme of study, root and branch, in the manner we are contemplating.
Do you know of any physics – or similar – departments/schools which have gone through such a major renovation?

Although it usually doesn't result in this big an adjustment to the curriculum, most academic departments in the US conduct periodic (e.g. once every five years) "Program Review" of their undergraduate and graduate degree programs.  There are many books and articles on how to conduct a program review.

You might want to take a look at Germany (and possibly other countries an Europe). Due to the Bologna reform, physics departments (and many other ones) were forced to switch their curriculum from the old diploma system to a bachelor–master system somewhere around 2005 (the exact year depends on the university).
At least my university used this for some restructuring of the contents and, e.g., did the following (just to give you an idea):

Introduced separate math courses for physicists (before, students of physics and mathematics attended the same courses).
Introduced special courses each for IT, presentations and numerics (before, students were supposed to learn this by themselves on the way or when they actually needed it)
Moved theoretical mechanics and electrodynamics one semester earlier.
Merged the courses on atomic physics and condensed-matter physics as well as the courses on nuclear and particle physics.

Other universities might have undergone even more radical changes.

It's not physics, but a cousin at least: if I remember correctly, the MIT Mechanical Engineering department went through a major restructuring of its courses about 10-15 years ago, in which they changed nearly the entire undergraduate curriculum.  I can't find any material about it online, but you may be able to to contact people who were involved to find out more.

My answer is only tangentially related to your question, but you may want to see if there are documents produced by some of the relevant professional organizations that outline how a modern curriculum should look like. For example, in Computer Science, this is the normative document: https://www.acm.org/education/CS2013-final-report.pdf . If such a document existed for physics, it might very well make your task vastly simpler because at least it already outlines what most of your courses should be about.

Such documents exist in engineering fields because of the horrible business of accreditation of engineering (and CS) departments. There's no organization accrediting physics departments, as far as I know, so I expect there's no curriculum guidelines to follow.

Let me revise my comment: there is an accreditation process for physics departments in the UK, and the documents are here. They may be of help to the OP, at least in deciding what material needs to be taught.


text:
How is a Coursera exam typically conducted?
Many Coursera online courses have an exam component.  This raises the question:
How is a Coursera exam typically conducted?
It seems non-obvious to me how one would conduct an exam involving students who might be on different continents.

Having not used Coursera, I do not know what tools they use. However, I have been a part to online exams from both the student and instructor perspective using the Blackboard learning management system. I suspect that features like many (if not all) of the ones Blackboard supports are present in Coursera.

Time limits - The instructor has the ability to set a time limit to the exam (which discourages web browsing to find answers). The instructor can also choose to force the student to complete the exam in one sitting or allow students to leave and return.
Flexible scheduling - The exam does not have to happen at a specific time, but may be accessible over a time period, perhaps 24 hours or more. The instructor can still enforce time limits and so on.
Lockdown - The implementation of Blackboard my institution uses comes with Respondus Lockdown (there are other products), which prevents students from navigating away from the exam once it is started. These products can also prevent such things as minimization of the window, opening new tabs, etc.
Proctoring - I have proctored an online exam for another instructor. I had to enter my credentials and a code before the student could start the exam, and I had to enter a different code when the exam was completed.

Features like these give instructors flexibility in offering the exam to students around the world, while still making it harder to cheat.
They will "cheat", however. No online course management system can prevent the student from using their text, notes, or another computer or electronic device to look up answers. The best defense against infractions of this nature are well-written tests (the kind you might write for an open-book or take-home exam).

@xyz - Thanks for the feedback. I mean cheating in the sense that students are not doing their own work and then submitting claiming that it is theirs. They do it in my bricks-and-mortar classes, so why should I expect them not to in an online course? The difference is that my bricks-and-mortar exams are proctored by roving human beings on the lookout for cheating. A student who cheats on my homework (which I am incapable of policing) will do poorly on my exam. If it is all online, you have to write better tests so that the answers cannot be found via Google, Wikipedia, etc.


text:
Is there something like a "peer-review paper"?
Journals like CVPR (IEEE Conference on Computer Vision and Pattern Recognition) have a peer-reviewing process. Depending on the journal (or the publication published after a conference - is that also called a journal?) one might simply know that all articles were peer-reviewed.
However, those reviews are not publicly available as far as I know.
This is also a problem of arXiv / bad journals. They might have (many) good articles, but one has to check them. A work-around might be to look at citation counts / who cited the article, but citations are not necessarily positive.
Are there any typical / recommended ways to write reviews and make them publicly available?

I'd be very cautious about publishing your reviews. Any review leading to a rejection is going to annoy some people and there's a decent chance this will come back to haunt you -- when those same people review your paper or grant application. I also think it's discourteous toward the authors of the paper: you're pointing out everything that's wrong with it and give them no chance to respond.

@user2898391 I think there are ways to fix the problems you've mentioned: Anonymous reviews, first sending the review to the authors, formulation of the review itself, a change of "reviewing culture".

@moose Stack Exchange sites are here to answer reasonably scoped, well-defined questions, not to discuss how to change the culture of an area.

@DavidRicherby I know what StackExchange sites are designed for. I never said we should do so here. In fact, I never said it should be done. I only said that the mentioned problems can be fixed and explained 4 ways to do so.

Depending on whether you want to leave short comments on papers you weren't invited to review or make public full reviews of papers that you were, you might look at http://www.pubpeer.com and http://www.publons.com respectively.

Or if you want the reviews on your own submitted manuscripts to be open, there are places like http://f1000research.com/

Since you mention the arxiv, you might be interested in Episciences, which aims at enabling what you describe, although I don't know what the current status of the project is.


text:
Wrong article submission
I submitted an article in a Reputed journal in mathematics.  It is in review process.  After 4 months, i realized that there are some trivial mistakes...   Article is still under review with journal.   What should I do?

If I have a corrected version, should I send that one?
Or should I share this situation with Editor?

I am feeling very bad because of me editor and reviewer are (will be) wasting their time with wrong article...

Trivial mistakes, by definition do not matter. It really depends on the magnitude of the mistakes. Are you talking typos or that "experiment 2" is missing.

You should do both. Namely, send an email to the editor, explain the error and how you fixed it, and attach a revised version, and ask them how they would like to proceed. They might

Send the revised version to the referees
formally "reject" the incorrect version and consider the new version a resubmission
reject the incorrect version and the corrected version.

In any event, you must contact them.

I think it depends to some extent on the magnitude of the error, and the complexity of the correction.
If you have found a serious error in one of the results, and the correction involves major changes to the proof, or requires a significantly stronger hypothesis or weaker conclusion, then I agree with the other answers that you should contact the editor and ask that the corrected version be sent to the referee (include a list of the changes you made).  Otherwise the referee may waste a lot of time sorting it out, or just reject the paper.
If you have found some typographical errors, or a stray factor of 2 in a constant, or omitted an obvious hypothesis in a lemma, then I would not bother the editor and referee with it.  Minor errors like this should not affect the acceptance of the paper; the referee should have no trouble realizing what you meant (or may overlook it completely).  If the paper is accepted, you can include the correction with any other revisions requested by the referee (as before, include a list of all changes).  If the paper is rejected, it wouldn't be because of these errors, and you can simply fix them before submitting to a new journal.
You'll have to decide where your corrections fall between these two.

First of all, when you send a Journal to review, is not a trivial matter, and you must be sure all the math is correct, that is the reason you are supposed to have it checked by colleagues and people who can give you thoughtful insight, it would come as unprofessional to an editor if suddenly an author says: "sorry I made a mistake, lets do it all over again"
In the best case scenario, the mistakes will be so trivial that the reviewers will realize it and accept it given that you correct the mistakes.
In the worst case scenario, is because of these mistakes that the journal would get rejected.
You can always try and resubmit, put I would try a different journal.

Of course one should try to get everything correct before submitting but everyone makes mistakes, especially small ones, and that's what the question is about. Withdrawing the paper and sending it to a different journal just because of a few trivial mistakes would be a massive overreaction and would waste whatever time the reviewers have spent.