text:
When can/can't I upload full-text to researchgate?
I just joined research gate (finished PhD in December - published 3 papers early this year) and as soon as I made an account, it shows that someone requested full text of one of my papers 20 weeks ago.
Am I allowed to just upload the .pdf? What are the rules there and how will I know if/when it is appropriate?

@EnergyNumbers possibly, but that's restricted to only papers already published OA, which doesn't immediately seem to be the case here.

@Andrew the answers there completely answer the question here.

This is entirely dependent on the policy of the publishers - there is no single general rule. For example:

Cambridge: no (but you can upload the submitted version)
Elsevier: possibly share the manuscript, but not the final PDF
Springer: accepted manuscript only

You can see most journal policies through the SHERPA/Romeo site. Note that some (eg Cambridge) have explicitly different policies for institutional or subject repositories versus commercial sites like ResearchGate.
The big exception is if your paper was published open access with a Creative Commons license or similar, either through an all-OA journal such as PLoS ONE or through a 'hybrid' OA option. In this case, you can repost it anywhere you want without permission.

ResearchGate also offers you the option of directly sending a copy of the paper to the person who requested it.  Depending on the publisher's policy it might still be a violation to do this, but it's somewhat less egregious than making the paper publicly available on the web.

@BrianBorchers that's probably acceptable to all publishers, IME (most institutional repositories have this workflow and I've never heard of it being challenged). I didn't realise RG provided that option, though, rather than hassling authors for fulltext.

You get a request to upload your full text, but if you follow the link to ResearchGate it gives you two buttons- one to upload the full text and one to send the full text directly to the requester (and you can attach a nice note explaining why you've sent it privately rather than publishing it on ResearchGate.)

@BrianBorchers neat, I'll be a little less rude about them now ;-)


text:
Master degree and PhD in biomathematics
The following question was posted on Math SE, but seems to be more related to Academia SE:
Next year I will start studying maths at university. I'm highly interested in biomathematics, but in my country there aren't specific courses for students. At least there are very few Ph.D. programs. So I'm thinking of taking a 3-years degree course here and then a Master degree and Ph.D. in another country. Are there such courses in UK or US? If so, which are the entry requirements (in terms of, say, English language certificates, couses taken, etc)? How can I prepare to such courses? Are there any suggested readings?

I know that pretty much every credited and decently reputable university has some sort of bioinformatics or biomathematics program. Even the school I currently attend, Indiana State University, which by the way is an absolutely shit school for ANYTHING except business adminstration, aviation and education, have a masters level bioinformatics degree, though I'm unsure about any PhD program. However, I know that Purdue has a program for it's computer science BA students to have what is called a "focus" (very common in majors like CS because of the breadth of where you can take it- also, criminology is very common to have 5 or 6 focuses as well) in bioinformatic data systems, and you can then pursue a masters or PhD with said focus.
Basically, even though none of that really answered your question, pretty much every university you go to will have some sort of bioinformatics / biomathematics (which by the way, I don't know if they're the same thing because I've always heard it called bioinformatics, which is the math behind biology... so I'm assuming there the same thing) program, and if they don't, they will DEFINITELY have CS / Math programs that are completely relevant to the study and very easy to get you into grad school on the basis of the only thing you didn't learn about bioinformatics was the application of principles you learned from your math classes to said field.
Also, most universities here in the US don't have specific requirements for transfer students beyond language certification. I.e., if you can speak decent English, which you can, then you'll be fine. Most of the Arabs in my Econ & CS classes right now can't speak a word of english at all and they're here so you'll be fine

@usεr11852 you're right. Bioinformatics, from what I understand now, is the study of processing biological data.
However, I still contend that the fields are interchangable. Many Computer Scientists could very easily change there major to some sort of mathematics (though not all) in the final 2 semesters and still graduate on time due to the interconnectedness of the two. All computer scientists are part mathematicians, and at the PhD level nowadays, all mathematicians are part computer scientists. I'd wager the two fields are roughly the same

I believe Coursera.org has a few MOOCs in biomathematics (or at least courses very closely related to it).

Hi, Jochen. This really doesn't answer the question—the OP is referring to "courses" in the sense of "major," rather than "lecture."

"How can I prepare to such courses?" - Guess my answer points to a way that one could prepare for this kind of courses...

Bioinformatics is a bit of a collective name for many different cross disciplinary research fields. Essentially it's biology, mathematics, statistics and programming blended into a dough, and baked together. Consider bread, using the same ingredients you can make many different types of bread in the end.
It's more or less the same with bioinformatics/biomathematics. I am a last year bioinformatics PhD with less than 6 months to dissertation. So far the people I have met that do similar work as I do, I could probably count with fingers on one hand. :)
Instead of considering fields, and courses and programmes, consider which skills you want to acquire and what subjects you want to work on. Essentially, the question boils down to what do you think is cool? Are you interested in RNAseq, or GWAS? Are you interested in doing SAM, or pathway dynamics? Perhaps signal processing for MS-based proteomics?
There are literally thousands of interesting problems out there that require serious bioinformatics efforts. Which program you studied is a bit irrelevant as long as you have the right toolset of skills.

In Sweden there are many universities strong in bioinformatics. The requirements are not very high (they depend on the program), and everything is in English and free for UE citiziens.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Can i shift my subject from Chemistry to IT
I have completed my gradation in leather engineering. But i would like to do M.Sc in Information Technology or Software Engineering or computer science or bio medical engineering or bio engineering.
I am working in software firm as well as freelance software developer. I have one software related publication & other two  environmental chemistry related publication. But now i'm really enjoying software development & i would like to do my M.Sc/PhD in these subject .As i wont like to do anything that actually i don't like. But will university accept me if my would like to shift myself from chemistry background to IT?

I actually know a large number of PhD chemists working in CompSci -- myself among them!

Of course you can!  Especially since you have an IT related publication and it seems you have shown interest in the field. I would highly recommend finding a supervisor with a project that appeals to you. It's all about your relationship with them for a positive graduate experience. If they want you and have funding for you, you will have much better chances of getting into the school you want to work on a project that excites you.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
How to add citation for the whole section of a report?
I'm preparing a report for the company where I work and the whole section in a chapter of the report (the theoretical part) is from a text book. Of course I've summarized the book but the whole section is from that book.
How should I cite the book?

I don't understand whether you paraphrased (restated in your own words) or reproduced (quoted verbatim) the book section.
If the former, just start the section in your report with something akin to: "The following section is based on Smith (2006, pp. 98-99)."
If the second, clearly mark the whole section as quotation (e.g. with quote marks and indentation), and append the correct reference:

"Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent massa turpis, luctus eget sapien et, posuere sollicitudin massa.
Morbi eu velit nunc. Aliquam consequat sagittis nibh, quis dictum nisi tempor." (Smith 2006, pp. 98-99)

That said, overly long citations or paraphrases usually indicate that you failed to distill what's relevant and apply it to your specific context. I'd consider rewriting your section with a clear idea in mind of what you want to convey and why.

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


text:
How to prepare for a meeting regarding a Ph.D. program I'm wait listed on?
I am on the waiting list for a Ph.D. program I applied to. I sent an email indicating that the program in question is my top choice and that I am interested in discussing my qualifications.
In reply I received an email asking whom I see as potential advisors.
The reply also indicated that the department is looking in to some of the issues I discussed in my application, and that there are multiple things to consider including how well research interests match, funding and time constraints.
I've set up a meeting with the person to discuss these topics. I've already updated my list of potential advisors, but there was not sufficient time to contact them.
How should I prepare for this meeting?

For each faculty member you would be willing to accept as an advisor, know at the abstract level what their recent papers are about.  Search for grants they just received to determine what areas they may be hiring in.
In the meeting, express enthusiasm for all of these subjects and describe how your background prepares you to work on them.
It sounds like this department has space in only one or a few research groups.  You have no way of knowing which group(s) that is.  If you want to get in, you should market yourself as suitable for as many groups as you can.  It is normal for the openings available to vary by chance and for you to have no information about it; much is left to chance in graduate admissions.


text:
Citing a book vs citing the original paper
Books often have great overviews of topics and can cite dozens of papers in a single section or chapter and the book author typically cites the original discoveries of many others besides himself.
Is it ever appropriate to cite a book alone, or should I always cite the original papers?
Does it matter if my use of the the material is a brief reference to a broad topic I'm building on vs a specific paper?
Is the number of years that have passed, or perhaps how common the knowledge is in the field a factor when deciding to cite the book or the original paper?
Does the answer vary by field? If so, in my case I'm typically working with robotics and computer vision papers.

I think it can be appropriate to cite a book, exactly because they can provide a great overview of a topic. I can think of a some cases in which you can cite a book. First of all, you may want to point the reader to further background material of your field of research (say, in the introduction of a paper).
Another example: Say you are in -some research area- and you want to use something that is common knowledge in -other research area- citing a book may be helpful because they can contain more background and better explanations.
Finally as you already mention, if the result is very old finding the original paper may be hard (for both you and the reader). Furthermore the exact phrasing of a results changes somewhat over time, so it may be more difficult to read.

Or for old enough articles, written in Latin.

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


text:
Does the admission committee for graduate studies look down on foundation courses
Many universities do not accept international secondary school qualifications unless there is an agreement between countries. The agreement I think compares the standard used in the country of the university (e.g. GCSE A-levels or SQA (Advanced) Highers in the UK) with the qualifications of another country.
International Students with unaccepted qualifications are given a conditional offer in some UK universities. The student has to do a "Foundation Course in ......" in an institution affiliated with the university (an "International College") and by passing with a certain grade, they go to 2nd year of a 4 year bachelor's degree or to 1st year of a 3 year bachelor's.
Beside the topics related to the degree, the foundation course focuses a lot on academic skills such as writing, presenting, note taking etc..
On the university transcript, the first year appears as a "credit transfer".
My question (finally), does the admission committee look down on such certificates even if the student got the bachelor's degree with a high GPA?
If it makes a difference, I would appreciate it if answers are given related to: 1- entry to MS degree 2- direct entry to PhD.

In general, if the GPA is high, this shouldn't be too much of a big deal. Normally I would look upon such a class as equivalent to an introductory-level course, and would not "look down" upon such a course. If the grade in such a course is poor, however, that could affect the decision.
If you are concerned about reviewers at another school evaluating this course appropriately, you could always include a note about it somewhere as part of your application (either master's or PhD).


text:
Is it Illegal to Share Student Work
Is it illegal for professors to make copies of or share student work with other professors without permission? This has happened to me. I thought there was confidentiality in academia but then again nobody follows the law or rules in this world.

To answer whether or not it is illegal would require very detailed knowledge of your local laws (you don't say where you are) as well as any agreements that you have made with your institution. As such you are unlikely to get a definitive answer. You might be able to change this to a more answerable question, such as "how should I respond if my work is shared without permission?" or something along those lines.

Note that while you may not have given specific permission with respect to that piece of work, at many institutions you sign a general agreement that states that the work you produce while studying is the intellectual property of the university.

To get a meaningful answer you need to share your location (at least the country) and ideally some specific details about the nature of the work that was shared, who shared it with whom and for what reason.

If you're in the US, this might be helpful: https://en.m.wikipedia.org/wiki/Family_Educational_Rights_and_Privacy_Act

P.S. If there are sensitive details involved, you might want to post from an anonymous account. Your current profile reveals your identity.

@DanRomik  Thanks for the services. I have deleted my email from my account. This seems sufficient.

@DanRomik Undergraduate, United States.

Thanks. It still matters a lot who the work was shared with, and why. The professor who was shown the work might have had a legitimate educational reason to see the papers, in which case it would not be a violation of FERPA (as far as my understanding goes, but IANAL). For example, a professor might show their department chair the paper of a student they suspect of cheating. So, your question still doesn't have enough details to give a meaningful answer I'm afraid.

@DanRomik I think I have enough details to provide a meaningful answer. It just would have to be a general, academic answer. This is fine; I am not interested in pursuing anyone legally.

@DanRomik - Why don't you post an answer for the U.S.?  This could at least be useful as a reference point.

@aparente001 no thanks. As I said, there isn't enough information to give what I would consider a meaningful answer. I'm interested in concrete questions, not in writing prompts for an academic essay. VTC'ed as unclear, but if OP provides more info I may reconsider.

@Insulin69 - What kind of work was it that was shared?  Was a reason given?

It is perfectly clear what is being asked.


text:
Grant funding for independent researcher with no past track record
I am an independent researcher working outside of academia with no past track record so far. Is it still possible to apply for research grants anyway, and how should I go about doing so?
I do have a very good research plan, but the catch is, I need some funding before I can carry them out. How can I convince grant agencies to give me a chance?

Can you edit your Q and expand on what "...no past track record..." means (relevant degree, publications, affiliation etc), since that is essential to answer your question? What field are you in?

In the US, to apply for NSF grants, you need to have an account on their FastLane website, which in turn can only be created through an established institution with an office of sponsored research or whatever it might be called.

Ok, this is going to sting a bit, but, practically, this is not going to happen, no matter how brilliant your research idea and plan is. In practice, the scientific credentials of the proposal author / proposed principal investigator are very important to project / grant acceptance. Having no affiliation with a well-reputed research institution is already a strike against you, but not having a track record is a knockout criterion for each funding agency I am aware of. To give you one concrete example, the Austrian Science Foundation (FWF) will, according to their published rules, not even scientifically review a proposal with an insufficiently experienced principal investigator. From what I have heard, other agencies have similar formal rules. In short: you will need a co-proposer with sufficient standing in your field, otherwise you are essentially wasting your time preparing the proposal.
Maybe this seems unfair to you, but try to see it from the point of view of the funding agency. While you may have strong confidence in you and your project, you are a huge risk factor to the agency. You have no demonstrated experience in leading a project, maybe not even in participating in one, you are not embedded into on of the traditional research environments, you do not necessarily have the resources to even conduct the research project, and, from a legal point of view, if you just take the provided grants and run away, there is no organisation that the funding agency can sue to get their money back.

There's an enormous range of different types of grants.  Some are from large government agencies that are correspondingly bureaucratic; others are from private foundations that may take an idiosyncratic approach to deciding who to fund.  So the answer may depend on what sort of funding you are looking for.  To a first approximation, it will be difficult to get government funding as a truly independent researcher (without some affiliation with a university, non-profit agency, think tank, industrial lab, etc.).  That would be the first place I'd start, by trying to get an affiliation that would allow you to apply for grants through an established institution.  If you can't convince anyone to let you do this, then your grant application is probably hopeless anyway, and if you can, then it will be a big help.
A second issue is how literally you mean you have "no track record".  If you have a minor track record (e.g., a degree and some publications in related areas), then it might be possible.  If you literally have no track record at all (no relevant degree, no history of related work, no relevant prior accomplishments, nothing), then it will probably be impossible to get a grant.  Even if you have a great idea, there would be no evidence that you are actually capable of carrying it out.  Maybe it's not strictly impossible - theoretically you could present an idea so obviously great that merely coming up with the idea would itself be strong evidence of competence - but it's highly unlikely to be worth the effort of applying if you have no track record at all.

I interpreted as literally no track record (hence my more negative answer below), but maybe that was not correct.

Again, depending on what you mean by "No Past Track Record", this is going to be hard if not impossible.
Many granting agencies, in their grant reviews, have a section on the environment/institution/etc. Essentially, this is asking "Are you in a place that can get this research done". And it often extends to more than just practical questions - do you have institutional support? Is there a sufficient mentorship scheme for new investigators, etc.
For most of these, many grant reviewers will look at an entirely independent scientist and say "No." Or score you rather poorly, which in today's funding environment is essentially the same as saying No.
Depending on how much you need, there are however a number of Kickstarter-esq crowd funding platforms for science. These might be a place to make your case directly, if the amount of money you need is modest.

Likely not.
I had grants as a "gentleman scientist", but in close co-operation with laboratories where I previously worked as a post doc. Same professors who already had multiple publications with me wrote the grant applications, not myself. There was no salary but we got access to supercomputing facilities. It was United Kingdom.
Such an adventure is fine to try for several months to fill some gap in the carrier, but without salary is not sustainable for years.
But your situation looks worse. Without trusting and collaborative professor behind, I do not think it would work. It seems even not transferable, or maybe country dependent, because when I attempted later in Swiss laboratory with no previous connection with me, they refused to start the talk. Hence worked for Free Software Foundation at that time, not much but OK, servers, task, co-ordinated development were provided.


text:
How should I mention the period between the end of my post-PhD and the beginning of my work as research staff?
I finished my post-PhD, after two years working under a scholarship, in April 2015. In September 2015 I was notified that I was accepted as research staff in my institution (I applied in December 2014). In September 2016 I was finally added to the "payroll" as a staff member.
Between the period April 2015 - September 2016, I kept receiving my post-PhD scholarship in what is known in my country as an "extension of the post-PhD". This is done because the time that passes between the end of the post-PhD and the final addition of your name to the payroll (if you are accepted) is rather long. In my case it took about a year and a half (which is the standard period), and this way one is not left with no monthly income.
The question is: how should I describe that period in my CV? Anyone from my country will be able to tell immediately what happened, but I'm not sure how to explain this to people from other countries.
In rigour my post-PhD ended in April 2015, so I can't really say I was working on it for an extra 1.5 year. What I did for that period of time was what I do now: research. But I can't say that I started working as a researcher after April 2015, because my first actual paycheck as such didn't come until September 2016.

In that period, if I understand correctly, you're just doing the job like you did after September 2016 right? If that's the case, you can keep one job description but with different funding source: XXX Post-PhD research fellow (funded by YYY scholarship from Apr 2015 - Sep 2016); then XXX Post-PhD research fellow (funded by ZZZ organization, Sep 2016 - Now).

It's the same organization which founded my post-PhD scholarship, the "extension" of that scholarship, and my staff member paycheck. Also, I think you understood the dates wrong. My post-PhD occurred in the period April 13 - April 15, then the "extension" May 15 -September 16, and finally the staff research position Sep16 - Now.

What are these things called in spanish?

With a somewhat uninformed opinion not knowing the particulars of what is common in your country, it seems to me like an "extension of a Post-PhD," which I would call in the US a "post-doc" or more formally a "Postdoctoral Fellow," "Postdoctoral scientist", or "Research Associate," is indeed that: an extension of a post-PhD, so still part of that interval. How does the type of work you did as a post-PhD differ from what you do now ("research") and in the "extension" interval?

AnonymousPhysicist "Posdoctorado" (post-PhD or post-doc), "Extensión de posdoctorado" (post-doc extension).
@BryanKrause the extension of the post-doc is not necessarily related to the post-doc. In my case I used that time to research a topic that was not directly related to the post-doc. Thus, it wouldn't be correct to simply say that I was enrolled in a 3.5 year post-doc. I have to mention that period separately to be accurate.

@Gabriel I would probably consider that a second, separate post-doc, then - is there a reason you think this is incorrect or not appropriate? E.g., "Posdoctorado, Dr. X Lab, University of Excellence, April 2013-April2015" "Posdoctorado, Dr. Z Lab, Another University, April 2015-September 2016" If this is common, do you have other colleagues who might have had a similar path? Can you ask for their CVs?

It's not a second post-doc either, since I did not enroll in a second post-doc and I was not given a scholarship for a second post-doc. I haven't asked yet because I wanted to gauge how this situation was understood by researchers not from my country. I can see that, expectedly, it is not easy to explain/understand.

Apparently not - is the "extension" essentially considered a form of government assistance? Are there stipulations on what you do while receiving the extension funding? You chose to do research, but could you have also sat home until you became staff without penalty (besides missed opportunity to do research, of course)? Otherwise, I don't understand why an extension doesn't count as another post-doc or a continuation of the first. If a research grant is renewed for an additional term, it is effectively a new grant: there was a second decision to provide the funds.

I did my postdoc under a government agency scholarship (2 years). Midway during that postdoc I applied to a research staff position (to work for the same agency). When the 2 years of the postdoc ended (April 2015), that same agency "extended" that scholarship until I could take possession of the research staff position (September 2016). In the meantime i was expected to do research, not necessarily related to my postdoc topic, but also not something entirely different. The 1.5 year period is most definitely not another postdoc, perhaps calling it a "continuation" is as good as it gets.

In the comments you said it is called an "Extensión de posdoctorado".  It is fine to list that phrase as your job title during the period.  It is reasonably clear to english speakers.
People reading international CVs expect to see unfamiliar terms and career progression.

I would avoid putting months on the CV.  Just use years.  It's a very small minority of hirers who still push for that exact info like some detectives searching for gaps (as if that were some embarrassment to root out).  That way, unless you have a gap that is a ful calendar year, it won't show.  Those who care can ask for it or do an application.  But this is just going up on a website for now regardless.
There is nothing wrong with just calling the extra months as a postdoc or researcher.  Whatever works better for presenting you.  Sounds like you didn't get the title/pay yet, but were doing the job elements.  Although I am mystified what is different in research done by a postdoc or individual researcher.


text:
Can anybody vouch for PubSure?
A few days ago I uploaded a pre-print to arXiv. Today I got an email from  a service called PubSure offering to evaluate the manuscript with AI (?) and give me a score on how "publishable" (?) it is. In their own words:

PubSURE is a super cool AI-powered solution that evaluates research manuscripts and provides a score to indicate their submission readiness.

I signed up to check it out (although my pre-print is already accepted for publication) and they ask you to upload the article (Doc and Docx files) to evaluate it (which I did not do).
I'm getting scam vibes from this one (but I could be wrong!). Anybody heard from this service before (perhaps even used it)?

Hmmm. If they call themselves "super cool" they are probably a scam.

Closing this as per this Meta consensus.

It's a scam.  Any service offering to provide you with a certificate you can send to a journal is a scam, because editors do not consider these certificates.

I can’t believe this question got closed when it was asked first

@gen-zreadytoperish Note that it wasn't closed as a duplicate - it was closed as it was asking for an assessment of a commercial service. The second question avoided that pitfall by being more general. The duplicate link was added afterwards.


text:
Why are authors not made anonymous during the review process?
During the review process of an article, the reviewers are (almost always) anonymous by default for obvious reasons.
Why are not authors also made anonymous?
It could help remove the weight that established authors carry in certain fields (which can tilt the scale in their favor), as well as the stigma associated to research coming from non-developed countries.
Are there any good reasons why this is not done? I can not think of any.

I wonder how field-specific this is.  While I'm not an h10 author, all of the papers I submitted in the field of learning science / analytics were double-blinded.  It did require multiple versions of the paper.

(Of course OP couldn’t have known it was a duplicate before learning the “double-blind” lingo.  So don’t see my close vote as a criticism.  It’s a good question, just one we’ve had exactly asked before in different words.)

@NoahSnyder I believe it is a duplicate. I was not even aware of the double-blind review system, which is why I didn't even mention it. Now that I know about it, I think that question precludes this one.

I have also voted to close as duplicate.

Sometimes they are. That's called double blind refereeing. It is becoming more common.
From https://www.maa.org/press/periodicals/guide-for-referees

The Board of Governors of the Mathematical Association of America has
  mandated that our journals use a double‐blind review system.

This blog post and comments discuss the history, pros and cons of double blind refereeing in  parts of mathematics and computer science.

I was not aware of that practice, thanks for pointing it out!

@BenLinowitz See the blog linked in my edit.

Some conferences and journals do employ "double blind" reviewing. Whether it is superior or not can be debated. Whether it is actually "needed" or not can also be debated.
But, single blind is just a tradition that makes some things easier on authors and editors. Double blind reviewing normally requires that a special version of a paper be presented for review, since the authors often refer internally to their own work and often use personal pronouns, such as "we". This makes it easy to disambiguate authors unless care is taken. There have been questions on this site about preparing such specialized version to avoid referring to essential early work by the same authors.
Double blind review also can narrow the set of acceptable reviewers. Often enough, a reviewer is chosen because their own work is mentioned in the paper, making it more likely that the reviewer will actually know of the work before being offered the paper for review. While some conflicts of interest can occur, these are normally pretty rare and can be handled via communication of rules for reviewers.
So, if an editor or conference committee agrees that there is little to be gained by double blind review and wants to avoid extra steps, they will likely just follow the traditional practice.

Yes, anonymizing the manuscript is a complication that I did not think of.

to anonymize, we just need to remove the authors name, acknowledging part, and rephrasing ‘we’ terms that refer to authors previous work. And again, even if the paper is accepted in one round, during final version submission (irrespective of journal and conference) authors can easily put these things back. Thus, what  @Buffy says anonymize manuscript is complicated, does not make any strong point here.

@user199, you describe the common case, of course, but not all are so simple. There have been questions on this site from authors with more complex papers for which it is harder.

@Buffy, I do agree that anonymous authors can easily be determined (or say the author belong to which group) if the experienced reviewers are aware of the previous papers written by the same authors — in some cases, the reviewers can guess. According to me, anonymity does not have any good impact on the review process; consider the case CVPR 2019, an AI-related conference, the number of submission was beyond 5000, this year CVPR 2020, the number is already reached 10000. How to find reviewers— a good question. Although it is a different context what OP asked.


text:
Original data vs reference data?
A journal asks to upload/link the data and code used in your article. I have a Github repository with data and code. One of the questions in the form is:

Are you linking to original data reported in your research, or are you linking to reference data which is supporting your article?

and you have to select either Original or Reference. This is rather confusing to me. What would constitute "original data"? If I downloaded some data and processed, arranged, and/or classified it, is is still "original"? Furthermore, all data used "supports my article".
Could someone explain the difference between the two, preferably with examples?

Your guess is as good as ours. Ask the journal.

Louic is correct, ask the journal. I am only guessing. But my guess is, original data is data you produced. By measuring, collecting (such as surveys), or calculating it yourself. Reference data is data that comes from somebody else and that you are just citing.

This question was asked a long time ago but remains on the unanswered queue. The clear answer is "ask the journal." But, let's think for a minute about why this distinction matters. As the OP points out, when doing data science, one often modifies the data in some way, e.g., to discard outliers, to change the type of a variable so '7' becomes 7, to wrangle the data into a different form (e.g., I have done this on a dataset where every row is a protest, including a column for date it occurred, and I wrangled it into a new form where every row is a date and a column for number of protests on that date), etc. It is best practice to document any such modifications in the paper or an appendix. Furthermore, it's great if journals are now asking data and code to be available, as this will help a lot with reproducibility.
I've published several papers analyzing data sets (in biology, economics, sociology, criminology, and epidemiology). In most cases, the journal wanted to have access to the data and R code (I did my best to clean up the code and add comments to make it easier to follow). I was never asked if the data I uploaded was the "original" or "reference" but if I were asked, I probably would have said "reference" because I think of the "original" data as the uncleaned, unmanipulated data.
Of course, this means the word "original" is overloaded, because it can also mean "data that I myself gathered." But I think, to emphasize that data wrangling often occurs, we should also use "original" to refer to data that has not been processed or wrangled. Ideally, I would suggest readers upload both data sets, and the code that was used to get from the original to the new data set that was used in the analysis of the paper. Of course, this might be impossible if part of the processing that you did was to anonymize the data.


text:
Should we act as gatekeepers of the journals based on their reputation?
Initially in my career, when I was sent an article to referee my decision to reject/approve used to be influenced on how "good" the journal was (IF, SciMago's Q). I.e.: if the article was ok but the results seemed "not enough" for a Q1 journal, then I would advise not to publish there.
I no longer do this.
My current approach is: if the article is well written and the results are reasonable, even if they seem small or not entirely novel, I'll approve. My reasoning is that the researchers themselves should be the judges of whether the work is important or not in the field; the impact of the journals on the process should be restricted to publishing reasonable work and nothing else.
Do journals expect us (the researchers/referees) to filter out articles based on their status? If this is true, should we even care?
I understand this is a heavily subjective topic. I believe the discussion is relevant to the site, if it's not go ahead and close.

While one could argue that the editor is fully responsible, ask yourself what input you would want if you were the editor?

@JonCuster At point here. The reviewer should provide the editor with the information they need to make an informed decision.

Debasing all journals to the lowest common denominator does not seem to be in the best interests of actual progress.

How is it debasing if the article is properly presented and the results are correct? Why should we care about the prestige of a journal that not only asks us to review articles for free, it then charges us (a lot of) money for publishing and reading those same articles?

@Gabriel: Let's say you are a scholar on Gerard Manley Hopkins.  Let's think about how other literature scholars judge the state of scholarship on Hopkins.  One not too inaccurate model would be that they look at papers in Modern Language Quarterly on Hopkins, read them, and consider how interesting those papers are to be representative of how interesting current scholarship on Hopkins is.  If MLQ publishes a bad paper on Hopkins, that makes other literature scholars less interested in Hopkins research, meaning you are less likely to be invited to speak, fewer grad students study Hopkins

which means you have fewer colleagues producing papers you would want to read in the future (and the conference you attend may no longer be able to support a session of papers on Hopkins), and if you don't yet have tenure, your work is looked on as less important by association so you are less likely to get a job or get tenure.  So it's in your interests for the one or two papers MLQ publishes every decade on Hopkins to be papers that interest others in studying Hopkins.

Well the solution is simple: stop looking at MQL (or whatever journal) as a guarantee of "good" papers. The quality and impact of a work should not depend on wherever it was published. This mindset is what got us into this pitiful state of affairs where Elsevier makes billions out of our work

@Gabriel: If I read the entire ArXiv feed in my subfields, I would neither get any work done nor get any sleep.  There has to be other people helping me (and others simultaneously) determine which papers I should read.  If no one does that, then I actually end up reading only the papers of my friends and collaborators.

Handing over to a journal  the power to decide what research is important is clearly problematic, hence the current state of academia. Leaving aside the dozens of tools that exist today that can help you filter out articles irrelevant to your field, I'd much rather trust that researchers are able to  come up with a way to make new relevant results stand out on our own.

I voted to close. OP's comments (in particular to the answer by Especially Lime) show that OP doesn't consider this post as an actual question, but as a way to promote their particular point of view on the topic.

Why does it matter what I think? The question has 7 answers, many comments and 4k views. It certainly seems relevant for the users of the site

From my experience, I am surprised at this question.  It has happened several times that I have refereed a paper, recommended acceptance, and had the paper rejected pretty much solely because my recommendation was insufficiently enthusiastic.  It has also happened that I have recommended rejection on the basis that the paper was of borderline importance (relative to other papers published in the journal) and had my recommendation overturned.
This is actually quite a tricky matter, because different people write reports with differing degrees of enthusiasm simply because of their natural mode of expression, and it can be hard for editors to parse just how enthusiastic a referee is about a paper.
If a paper is important, I try to briefly explain why the paper is important.  If a paper is not important, I also try to explain that.  For papers somewhat in the middle, I find it helpful to give comparisons to other papers published in the journal or recent papers published in journals of about the same prestige as the journal in question.

This has never happened to me. My field works on a single-reviewer almost exclusively, and what they say usually goes.

@Gabriel: Yes - my field works on single reviewer also, but the editor is almost always someone reasonably knowledgeable about the subject area of the paper.

Yes, of course your recommendation should take into account how strong the paper is relative to the journal. This is information that the editor wants, and typically will not be able to assess as well as the referee can. It is also what other referees do, so by ignoring this aspect you may be giving undue advantage to people fortunate enough to get you as a referee.
In my experience the invitation to review will normally clearly indicate this. Here is an example from a journal I review for. (Of course, you might have your own opinion of how selective different journals actually are, even if their blurbs are very similar.)

In making your expert judgment, please note that [journal] is highly selective.
It is the journal's policy that manuscripts which do not contain a major
new research finding or a novel approach to [subject area], even if technically correct, should be rejected.

The responsibility of evaluating the paper's importance certainly should not rest with the author, since the author's job (usually literally) is to get it accepted by the strongest journal they can. The only thing that stops people submitting everything to the strongest journals is the expectation that referees will say "this isn't significant enough for journal X: try journal Y."

Although I understand your point and I opened this question to read other points of view, I will not be doing this ever (again). The journals are already getting my labor for free, they don't get to tell me that I should keep their "high selectivity" in mind. That's just giving them even more power and I refuse to do that anymore.

@Gabriel: That's an entirely foreign point of view to me, because the editors who ask me to review papers are almost always colleagues whom I respect or even friends.  Strangers whom I don't even know by reputation asking me to review get a 'No' by default.  Also, I do have a professional interest in giving more visibility to the best work in my field and giving less visibility to the not so good work, because people in other areas will judge my area of research by its most visible work.

@Gabriel I appreciate your point of view, but I think that in your case the appropriate thing to do is refuse the review request, rather than accepting it but not actually doing what they asked. (I should probably have prefixed my whole answer with "if you decide to review".)

I do know the Editors, actually I've published with some of them. I also think important work should have visibility. I do not think we should hand over the power to decide over that visibility to journals/publishers

@EspeciallyLime I will not be doing that. And I actively urge others to behave in a similar fashion. I wholeheartedly believe is ok the best interest of science to take power away from publishers

@Gabriel I don't understand how the normal model is "handing over power to journals/publishers". In fact it is the opposite: the journals are handing over power to the referees, subject to oversight by editors. Hence I intend to continue using this power responsibly.

Because that's how it works today. Journals are used as a benchmark of how important the articles that are published in them are, instead of judging the articles by their own importance. Publishers don't "handle over power" to us, they recruit our labor for free! My point exactly is to use our position as reviewers responsibly: by doing a service to academia and our fellow researchers, not to the publishers. Why do you think http://thecostofknowledge.com/ exists?

I'm sympathetic to your view of the role of the peer reviewer. I think the best information the peer reviewer can give to an editor, at least in the fields I work in, relates to whether the manuscript is methodologically competent and whether it deals with similar work correctly (shows how it fits into literature, doesn't ignore previous innovations).
I find it difficult as a reviewer to know whether a manuscript clears the novelty/impact bar, especially for some journals that I don't spend as much time reading. For me, the editor has the best judgment of what is important, interesting, and high enough quality for their journal. I generally assume they can tell whether the argument is important and novel, if it is correct. But they may be unsure of the correctness.
My reviews tend to focus on whether I believe the paper is accurately representing prior knowledge on the subject, doing something that follows logically from their take on that existing knowledge, and uses methodology that that is rigorous/adequately answers their questions. Sometimes I get stuff that seems fairly trivial but is otherwise very trustworthy. In the social sciences, we are often trading off between importance and quality of evidence so I try to tell the editor that the evidence is of high or low quality but they can decide whether the rest of it fits for them. If the work seems to be of especially high quality and importance, I will still mention that though...even if I may add a caveat that I don't intend to usurp the editor's judgment on such matters.

My philosophy has always been that a paper should be critiqued for it's flaws and compromising issues no matter what the impact factor of the journal is. We shouldn't let low quality, scientifically questionable work slide just because an impact factor is low. I treat all peer reviews equally.

Many a journal editor believes that a paper can be have no flaws or compromising issues,  and yet not be revolutionary enough for their esteemed title.

That should be the editors call. If it gets to peer review then the editor believes it's worthwhile at least to be scientifically evaluated.

Yes, we'll, I think that's the OP's point of view, but some editors need reviewers to tell them how exciting and ground breaking it is, because at big,  generalist journals,  the editors might not feel they know enough to make that call.  They only know it must be "ground breaking", but they don't know what ground breaking is.

My reasoning is that the researchers themselves should be the judges of whether the work is important or not in the field

I have spent a lot of time researching published technical research papers for accuracy and usability and validity. I never, in all of my years of doing this, have found any technical research from a certain extra large country to be of any use via any of their findings. Never. These were published in scientific journals that showed up in major universities in the United States of America. My guess, but it is still just a guess, is that some journals publish some papers from some sources because it makes them look more "inclusive" even though [if] the paper is trash.
Your question:

Do journals expect us (the researchers/referees) to filter out articles based on their status? If this is true, should we even care?

Due to what I just told you: They might expect it. But their actions do not support that. Should you care: Not really. Publish facts and honest conclusions and leave it to the reader to judge if the journal does not.
Industry commonly has personnel reading and studying and considering research reports in their selected support journals. Universities sometimes do the same. Some sources have for so long a time been a waste of journal space that they are almost automatically discounted and their articles not read. Some sources are so useful that their papers are sought out. Be useful. Do not worry about the rest.

One stop gap measure to address this and other problems with peer review is to make the reviewers public and pay them a fee from the journal company. This creates an open market rather than an arbitrary merit based socialist system of this research is better than that. But eventually, peer review needs to die off and arxiv.org with pubpeer should be the new model of publishing research.


text:
Two distinct papers solving same problem to same conference, allow update post-acceptance?
Authors A and B both submitted different full papers solving the same Computer Science problem X to a prestigious conference and were accepted. They each have clearly distinct approaches, studies, and novel contributions. The conference camera-ready deadline has passed, but the conference has not happened yet.
Is there any known precedent to deal (or not deal with) situations like this? Should special provisions be provided to allow the authors to update related works to reference each other?

Apologies about the vagueness of the title question. This one was hard for me to find the right amount of terse-wording.

Sounds like a pretty straight-forward case of simultaneous invention.
There's nothing wrong with these papers being published without reference to one another, just as though they had been submitted to different venues.  At the same time, if the conference wants to arrange for the authors to add citations to one another (as would likely happen if they were to be published in the same issue of an journal), then that would be a neat and elegant refinement that would probably benefit both sets of authors.  Moreover, the associated society publisher (e.g., IEEE, ACM), is likely to be able to handle arrangements without much trouble as long as they aren't too far into production of the proceedings.  Don't do it if only one set of authors can update, however: an asymmetric arrangement would inappropriately benefit one side over the other.
Thus, I would recommend making the extra effort if it's within reasonable bounds, but not going to heroic lengths if it will badly complicate things.


text:
What is a reasonable reimbursement time for conference travel from a department?
In my job before grad school, I could expense items as soon as I had a receipt and I knew exactly when the money would arrive (typically the following pay cycle). In grad school, it seems to be a mystery when I will receive reimbursement.

I bought tickets and airfare on day 1 of this scenario
I was not allowed to request reimbursement until 6 weeks later, after the conference
The conference ended, I requested reimbursement. 6 weeks later, still nothing!

So for the last 12 weeks, my account is down airfare and tickets, and for the last 6 weeks, I'm down the hotel, transportation, and meal costs. I've sent all the emails I can and have asked around -- the response I get is "The finance department does not give exact days of deposit."
Is this the norm in academic institutions? What is a reasonable reimbursement time for conference travel from a department?

At the institute where I did my PhD you could submit a request for an advance beforehand, based on a cost estimate. Also in some places the institute can order the airline tickets for you and then it does not have to come out of your pocket.

I've waited 7 months in my current lab. I'm not very happy about this as I just spent 2 months in the field and paid for a hotel for that time, and I don't want that happening again! But this will be an outlier. Unless you are in France.

Just my two cents.

Departments pay after they receive the necessary invoice from the student. So, they cannot pay hotels before you return from the conference.
In my department, buying the air tickets is not enough. I also have to provide the boarding passes that I actually used the tickets. That means you can only get the air tickets money AFTER returning from the conference. This makes partly sense, because if you got sick and cancelled the trip they would not have given any money to you in advance, so you would not have to return them back.
In many conferences (for CS), you get the registration invoice at the desk and not when you pay online. Again, this invoice is needed for getting back the money you paid, since most institutions cannot provide funding without invoices.
Logistically you might make a reservation in 2014 and the trip is going to be in 2015. Institutions cannot pay money in 2014 for an invoice issued on 2015. This might also occur for smaller logistic periods (every 3 or 6 months) as well, depending on the country's tax laws.

Bottom line. You should start counting time AFTER coming back from the conference. Expecting to be paid in advance without providing the proper invoices is simply not possible. After that, it depends on each department's bureaucracy on how soon you will get the money. And believe me six weeks does not seem that far fetched too.

Some departments, however, do have a mechanism for "pre-reimbursement" for things like registration fees and airline tickets before the trip takes places.  You typically then have to submit everything again afterwards, to prove that you went, etc.

@jakebeal You are right. Some departments have a "pre-reimbursement" mechanism but a) the OP did not utilized it (if his department has such a mechanism) or b) it is sometimes very  difficult to convince the "money-getekeepers" of the department that you actually deserve this pre-reimbursement.

Some universities even pay for some things, like flight tickets, directly. For others that you are reimbursed, but cannot afford, you may negotiate.

I know the boarding passes rule, but I have a feeling like this kind of thing is coming out of fashion. Partly because with the advent of e-tickets, the chance that you get an actual boarding pass at the airport (at least one that doesn't look like you had just typed it yourself in Notepad and printed it on the cheapest available paper) is decreasing, and also because with various means of transportation (that can easily be equally or more expensive as/than planes), there is no guarantee you get any proof of your journey at all (e.g. train tickets are only checked on some train rides).

@Davidmh: Unfortunately, even when a university has such procedures for its faculty and staff, students are not always eligible.

@NateEldredge in mine, PhD students are staff, and even master students can use it when it is tightly related to the program.

It is standard for departments to wait until after travel to process reimbursements. In fact, many require boarding passes or other proof that travel occurred that are impossible to provide before travel finishes. Some departments will reimburse before but this is (in my experience) the exception not he rule.
Reimbursements after the fact will vary based on the specific bureacratic rules for approval, the people doing the processing, and the backlog that the administrators are facing. I've had travel reimbursements processed in three days and in three months at the same institution.
Two general pieces of advice:

Remember that administrators are humans who understand that carrying the costs for travel can be difficult — especially for graduate students who are more likely to live paycheck-to-paycheck and carry these kinds of bills on their credit cards than faculty. I've made my situation clear to the folks doing the processing and had my reimbursements bumped to the head of the queue.
In the future, keep in mind that administrative assistants can often purchase plane tickets, conference registrations, and hotels on university credit cards. If cashflow is tight, look into doing this ahead of time to keep this situation from occuring.

"require boarding passes or other proof that travel occurred" - of course, in plenty of cases, you simply have no proof that travel occurred even after the travel.

While - as others suggest - it is standard for departments to only reimburse after travel, it is also customary in many (? / most?) universities and research institutes to advance some of the expected expenses upon request. This can involve some bureaucratic procedure, or could be very simple and based merely on the pre-existing approval of travel, but in any case you may very well get most of you expect to pay before actually paying it, or at least before traveling.
This balances out, to some extent, the annoyance of being payed the exact amount after the fact; and also makes it less of an issue if the university is late in concluding the payment of the final correct amount.


text:
What reference style is this?
Below is a reference of an article cited as footnote on a page of a book. I'm not familiar with this style so just want to know.
Anne Nguyen. Cultural and Social Attitudes Towards Mental Illness in Ho Chi Minh City, Vietnam. Stanford University Research Journal 2003: 27-31.
And here's a reference for a book:
Richard Keller. Colonial Madness: Psychiatry in French North Africa. Chicago: University of Chicago Press, 2007, 89.

Who is the publisher of the book? It may be a "house style."

Related question: How to know which citation style is applied?

The style seems to be a slight variation to Chicago notes style (as opposed to the bibliography style). In strict Chicago the journal article would be:

Anne Nguyen, "Cultural and Social Attitudes Towards Mental Illness in Ho Chi Minh City, Vietnam," Stanford University Research Journal (2003): 27-31.

With the key differences being a comma instead of a period after the author, quotes around the title followed by a comma and parenthesis around the year.
Similarly for the book it would be:

Richard Keller, Colonial Madness: Psychiatry in French North Africa. (Chicago: University of Chicago Press, 2007), 89.

with a comma instead of a period after the author and the press and year in parenthesis.


text:
Suggestions for a non-traditional interview?
I will have a post-doc interview in social sciences, warned to be a bit nontraditional in the sense that it will focus more on general logical capabilities and unique/creative thoughts instead of specific sets of skill or fit with a particular project. The reason is because this is a training grant I guess. Literally, they want to emphasize on "innovative" aspects of applicants, though I think that it's quite tempting and ambiguous.
So, I guess that I'd want to ask for questions you may have that can train the brain in this direction, some thing thought-intriguing like this:

What is the most significant finding in your field in the last couple of years and how does that mean to your specific work?

Any comments are welcome :) Btw, if you happen to be in social sciences, how would you answer the above question?

"warned to be a bit nontraditional in the sense that it will focus more on general logical capabilities and unique/creative thoughts instead of specific sets of skill or fit with a particular project."  It sounds like you are well aware that that could mean almost anything (or nothing: it could mean that they'll just pick whoever they like and don't want to be held accountable for why).  Did they really tell you this in such slippery, nebulous language?  Also, something seems conspicuously missing from the quoted dichotomy: won't they ask about your thesis work??

Also, your sample question doesn't seem nearly as spacey as what is presented in the first paragraph.  I can't say that it is a standard postdoc interview question in my field (e.g. because it is not standard to do interviews for postdocs in my field) but it sounds more than reasonable.  I wonder though how some other social scientist's answer to that question would help you out?

Well, they didn't literally say it could be "anything", but instead informed that the interview will mostly cover general questions.

I find myself scratching my head that someone could be looking for a postdoc who is an "innovative thinker" and would not try to ascertain this by talking to the candidate about what they've been thinking about and working on for their thesis.  I would think that would be the best way to get innovative thinkers -- much better than asking some weirdo on-the-spot question and watching in what manner the candidates squirms.  What do you make of this?

(This should attach to the previous comment, but it passes the allowed time) In the announcement, they want to find postdocs who can contribute to move the field forward in big leaps, not "baby" steps. I think it's more a product of marketing to secure training funds though. About the question, I just learn that you're in maths. I'm not sure whether mathematicians can keep updated with most advanced breakthroughs in the field, but in applied social sciences it's hard to tell whether some work is the most influential, especially in a short period.

Your last comment tells quite exactly about the atypical nature of this interview. A simple proof, there will be 3-4 interviewers and the interview will last only about 15 minutes! I don't think I can present half of my work and future directions in this time frame. Somehow it feels like how I respond is more important than what I respond. There's some chance to talk about the dissertation, but I believe it will not be into details as much.

Wait, what? The whole interview is only 15 minutes?!?  Is this an on-campus interview, or something that takes place at a big conference or somesuch?  In mathematics we use the term "cattle call" for the latter and generally acknowledge that such interviews need not amount to much.  It is hard for me to believe that anyone who has seriously narrowed down the pool to a small number of contenders would be willing to spare so little time interviewing them.  I am tenured so be careful listening to what I say, but: I think I would not have been so keen on this type of interview.

(To answer your other question: in mathematics there is a very small percentage of top work that everyone agrees right away will be huge: e.g. solutions of hundred year old problems and the like.  The average graduating PhD is not likely to be up on such earth-shattering things beyond the level of gossip/broad culture though.  I took the question to be more localized -- i.e., not field like "mathematics" but sub-subfield that the graduating student is working in -- and also more subjective -- i.e., tell us what is important to you.  I actually like this as an interview question!)

Yes, that's right. It's an on-campus, 15-minute interview. It looks like I will be toasted for a quarter of hour by 4 interviewers, who, by reading their bios, don't have reasonable levels of expertise on what I'm doing. This further enforces my thought that the interview will be different from otherwise normal ones. I wouldn't be keen on this formation either, but I've taken it since I know that, once in, postdocs have great opportunities to collaborate and develop career paths. It's hard to tell though whether previous cohorts of postdocs here have really done "innovative" scholastic works.

Well, you seem to have a realistic take on it then.  Best of luck: sorry I can't be of any real help.

15 minutes, on campus??!! boggle I hope at least it's local.  I can't imagine getting on a plane for that.

Without more information, I would not assume that they will not ask you about your research, publications, and dissertation.  Assume that they will.  My impression is that they want to go beyond this "CV stuff".
I suggest that you should spend more time to understand the motivations of the organization sponsoring the post-doc and why this is funded as a training grant rather than as something else.  Do they put special emphasis on making their research relevant to the real world (i.e. to policy makers, to the social groups being studied, to the general public)?  Do they aim to develop social scientists that go into non-traditional careers or interdisciplinary work?  What has this organization done in the past that they themselves call "innovative"?  Do they aim to redefine the boundaries and methods of social science?

Regarding how to prepare, there are plenty of books on creativity that have exercises that might stimulate this part of your brain.  But I'd guess that spending time on these books won't provide a good payoff for you.
A better strategy would be to organize a debating group with some peers.  They don't have to be at your university.  You could do it on-line via Skype or Google Hangout.  Arrange a meeting and specify an important+controversial topic in your field.  Focus the debate on how this topic could be researched in a new and different way, such that breakthrough results might be achieved.  For example:

Could the problem be reframed, rescoped, or redefined?
Could new methods be applied or existing methods be combined?
What new methods/approaches have already been tried but have failed? Why?
What methods or approaches from other disciplines might be adapted or applied to this topic?
What if this topic was researched at a much larger scale? much smaller scale? Over a long time period? At a single moment in time but in great detail?
How can research results become more compelling, rigorous, or widely applicable?

And so on.
Basically, your debating group will be exploring the space of possibilities just beyond what is being done today and assessing the prospects of improvement or innovation.
The value of doing this in a group rather than solo is that you will be engaging in the same modes of thinking and communication as the interview. You can and should challenge each other to clearly explain and justify your ideas, and to properly characterize them even if they are sketchy or "wacky".
You might find that this sort of preparation isn't for you.  If so, then maybe you might have to admit to yourself that you aren't an "innovator".  That's fine. There are many other good roles in social science that emphasize other traits and skills.


text:
What is a good scheme to determine percentage contributions to a paper
Sometimes researchers are asked to define percentage contributions to a paper with more than one author. E.g., usually the supervisor in charge of the project will determine in which percentage each of the researchers who coauthored the study contributed to it (in my institution the supervisor is left out in order to prevent abuse). These percentages can then be used to distribute per-paper publication bonuses or for other (usually administrative) purposes.
Which is a good scheme to fairly determine these percentages, considering the inherent difficulties in numerically quantifying intellectual work? Are there "standard" procedures to do it?

This sounds awful. Don't let the bean counters win.

Use the money to buy flaming torches and pitchforks, storm the administration building, and toss the policy into a paper shredder.

@StrongBad Whether it sounds awful or not this is what they do, and I cannot change it. Given that fact, I am looking for the most fair way to quantify how much each author contributed, so that, for instance, publication bonuses are distributed as fairly as possible.

I think percentages are bad practice, confidence intervals are much better. Or p-values with null hypothesis that the piece each author worked on could've been produced by a random monkey.

@MarcClaesen: you are joking, right? Please tell me you are.

@StephanKolassa I am 18% serious (95% CI [12%-25%]).

@MarcClaesen: thank you. Now I'll sleep better tonight.

The only fair way to do this is to have all authors sit together and figure it out. Yes, this can result in very awful situations, but it can also facilitate a PI explaining how much background work they he or she did or even explaining an insecure grad student, how much important work they did. Of course, if the atmosphere is loaded between some of the authors, this could end horrible. On the other hand, in that case there is nothing you can do to prevent them fighting over the decision in the end.

@MarcClaesen 93% of statistics are made up on the spot...

@Floris One of the few things that might become true if repeated often enough.

@TobiasKildetoft At which point it would automatically become false.

@Miguel Being true does not prevent something from being made up :)

This does sound awful. However, I understand trying to make the best out of a bad situation.
As you write, it is extremely hard to numerically quantify intellectual work. As such, I would strongly recommend going with an extremely simple weighting scheme, so as to minimize the acrimony of discussions that will certainly come. You don't want people to discuss why somebody got 15% of a paper, while somebody else got only 10%, because people are extremely fast in figuring out what this 5% difference means in $$$.
For each paper, get someone impartial to administer this. Then have all authors quantify everyone's contribution on a scale of 1-3. Don't go any finer, because anything finer is impossible. Let the impartial person pull all these together, average everyone's estimate of everyone's contribution and assign percentages based on the final number of points.
Advantages:

This is simple and understandable.
It requires no special software, apart from a few spreadsheets.
And it gets the job done.

Disadvantages:

It can easily be gamed. If someone consistently gives himself top marks, the impartial facilitator may want to have a discussion with this person.
How can a junior author, perhaps an undergraduate student, assess the contribution of the PI and how much time he spent writing grants to get the money?

So it may well be that this is impractical, given the disadvantages. In which case you may need to fall back on someone senior unilaterally assigning contributions.
In such a case, I'd again work only with three-point scales. If your scale only includes three possible grades, you can meaningfully grade contributions into "minor", "medium" and "major". Anything more fine-grained, like a four-level scale, and people will start arguing why they only got a 2 when they obviously deserved a 3.
Everyone, please feel free to point out further shortcomings in the comments.
(And: try to get this policy revoked. It is horrible. Either the bonuses are too small to spend much time on such a scheme, and to fight over it - and someone will always pick a fight over this, no matter how trivial the sums are. Or the bonuses are high enough to matter, in which case the fighting will be worse. Better not to give bonuses based on paper contributions at all. Scientists should be motivated to write papers for other reasons, like tenure or recognition, which still seems to motivate enough people to write but should have drastically lower chances of poisoning your work environment.)

I like this. A possible refinement would be that every author gives each author a 1-3 rating; it will reduce the reliance on a single person's opinions. And if I want to keep working with John I should probably be generous in acknowledging his contribution or next time I want help Is get a "no". Thus over time this self-adjusts. Incidentally a similar problem occurs when patents are written, especially in countries where inventors are due the royalties (even if they work for an employer). In those cases a lot of money can be at stake - not just a publication bonus.

When you say "get this policy revoked", what are you suggesting? Giving equal bonus portions to every author? Not giving bonuses at all (one of the departments I'm affiliated with doesn't)? Maybe I should point out that the bonuses are not big enough that people have actually been fighting over percentages.

@Miguel: I edited the answer to clarify what I mean by "get this policy revoked".


text:
How to react to your work being cited incorrectly or in a misleading way?
This morning when I opened my email I was very excited to find a Google Scholar update telling me of two new citations from two different sets of authors each to a different paper of mine. As usual, I immediately checked the papers to find out if the authors were praising or criticising my work (or perhaps they found a mistake in one of my papers!). To my surprise, in one case the authors wrote a misleading statement which resulted from stretching quite a lot some of my conclusions. In the other case, the authors simply made an incorrect claim (details below for the curious). It's not the first time this happens to me - I even got one citation completely out of context once. How to react to this kind of situation?

Details for the curious:

In the first case, the authors cite a paper of mine where I compare two different methods to calculate elastic properties of materials. My main conclusion is that one of the methods converges much faster than the other one with the size of the basis set - in other words, it's computationally much cheaper. For calculations with usual basis sets the first method is much more accurate than the second one, with disagreements between the two in the order of 10% or even 20%. They claim that I show that both methods agree within a 1% of each other, which is misleading at best, because for the second method to agree within 1% of the first one one needs to do a very expensive calculation. That is one of the main points of the paper and it got completely overlooked by the authors.
In the second case, the citation is plainly wrong. The authors cite my paper as an experimental work on InGaN semiconductors while it actually is purely computational.

Are you asking whether or not you can prevent them doing this or issue some sort of retraction, or how you should react to how it makes you feel to have your work misrepresented?  'How to react' could do with some clarification.

@Meelah The aim of the question is also to establish what depth of action is proportional to the "offence". So in a way you're asking me to answer my own question. I would not ask someone to retract their paper because of this, that seems quite extreme.

'to establish what depth of action is proportional to the "offence"' That's a clearer way of asking the question.

I agree with Boris' answer, but thought I'd point out that sometimes a plainly wrong citation is due to the authors not using an automatic citation engine (e.g., using Word instead of BibTeX) for a journal that uses numbered citations (e.g., IEEE journals). If you move text around (or delete text), it's easy for those citations to get off.

It is no different from finding any other mistake in a paper that you read --- just write e-mails to the authors politely explaining the errors. It is in their interest to fix them.

When the other papers are already finished, fixing is pretty hard to do.  It's not quite enough for an erratum.

@gerrit Even still, they should appreciate getting clarifications on what you did.  This could easily come up when they talk about their work and in their future work.

How about the five stages of reaction to grief?

Denial: "Hmm, that can't be right..."
Anger: "They're so stupid!"
Bargaining: "Dear Smith & al, in your paper Foo you cited my paper Bar saying that XYZ. I'd like to draw your attention to the fact that, in reality, XYW. Will you consider blah-blah-blah?"

and now it's either

Depression: "Oh no, they're not responding/not agreeing, I have to write the editor of the journal. :-( :-( :-("

or

Acceptance: "Great, they've agreed to fix it and write their own erratum for the journal to publish."

How to react to this kind of situation?

I think it depends on the context. For:

They claim that I show that both methods agree within a 1% of each other, which is misleading at best, because for the second method to agree within 1% of the first one one needs to do a very expensive calculation.

There is a risk that the literature is now misleading. You could reduce this risk with a clarification, perhaps in a technical report version of your work. A diligent third party can now establish the truth.
For your second case:

the citation is plainly wrong

You can probably ignore this, since it is a clear error, which should not mislead.

Unfortunately, misrepresentation happens all the time.  One tends to look for ways to prove they are right and someone else is wrong.  It is then left to the audience to decide whether or not they want to believe their interpretation of the work.  If one is made aware of the misleading or incorrect information, and one can, one should stand behind it.  Sometimes the facts are misinterpreted because they were not delivered clearly and decisively.  Therefore it may be helpful to include more information to clarify the work.  The purpose of receiving the google scholar alerts of citations in the first place is to guarantee that one's work represents correctly.  So as long as one can, and it matters, one should do their best to maintain the integrity of their work and the interpretation by others.


text:
Establishing the list of authors for a comprehensive/review (conference) paper
I am about to submit a paper for an international conference in condensed-matter physics. I want to present work which has been done over a number of years with different people. In particular, I want to include i) work that I did during my PhD with set of collaborators A; ii) work done also with set A but more recently; and iii) related work done also more recently but with a set of collaborators B.
In a way, this could be regarded a bit as review of methodology/older results plus new results, all in the same field/theme. All the results I will be presenting are already published in different journals, except for the work done in collaboration with set B which is under review at the moment (note that our conference culture differs from CS, where the conference is typically also the publication venue for the work).
My question is regarding how to manage the list of authors for my abstract. In the past I always presented very specific bits of work for which the author list was clear. In this case I do not know how to handle it given the more comprehensive nature of the presentation. I am considering the following options:

Use only my name as author and reference appropriately the relevant publications. Then acknowledge my collaborators with a slide at the end of my presentation.
Use only the names of the most important contributors to the work in the list of authors, then acknowledge everyone at the end of the presentation.
Use everybody's name, then again use a slide at the end with pictures etc. where the roles of the different collaborators are highlighted in more detail.

I am biased against 3. because of practical considerations: if I submit an abstract with lots of names then I have to get everyone to agree on the abstract's and presentation's contents. I am also afraid that 1. might come across as if I was trying to neglect the contributions made by others and could be unfair to them, especially those that contributed most.
I am looking for some advice on how to handle this kind of situation in such a way that the contribution made by everyone involved is appropriately acknowledged.

The way that I think about this sort of situation is that co-authorship of an abstract and talk is very low-stakes, and there's little reason to be stingy with it.  The most important thing here is to preserve a good relationship with collaborators that you value, and so I would recommend asking your collaborators.
If it's a collegial group with good working relation, then you'll probably get a quick consensus on one of the three options.  My own experience with many co-author situations like this is that many collaborators are happy enough to go along for the ride; a few will make constructive (or at least neutral) suggestions, and most just want to make sure their name isn't getting associated with anything embarassing---most people will only try to micromanage if you invite them to.
One important note, however: if the consensus ends up going with option #2, where some people get designated as "important", then let your collaborators decide if they should be on that list.  Again, the authorship of an abstract and presentation like this is pretty low-stakes (unlike for journal papers, where it's good that it sounds like you've already got clear boundaries drawn).  It's extremely dangerous for good relations if you put yourself in the position of telling Juan that he's less important to you than Marie.
Now, if you've got a problem collaborator who is not likely to be collegial or who is going to try to operate you like a puppet on stage, that's a different problem, and one whose resolution is likely to require very specific help and advice from some of your senior collaborators...


text:
Can I get into grad school with a low GPA?
So here's my situation: I'm a senior electrical-engineering major student in a decent-ranked university (60-80), and I've been working in a lab in our department and published 2 papers as the second author (conference paper, IEEE) and currently I'm in charge of two projects so I may publish more before I graduate. The thing is: I have a low GPA (2.9), but there is a reason: I've been an athlete of the fencing team in our university, and for two years I've been the vice captain of it. I have to go to practice every night, Monday to Thursday, so I don't have a lot of time to study. My boss, who got her PHD degree from CalTech, trusts me a lot so I will have a kickass recommendation. She refers me as a student who's "not very good at theoretical learning, but always creative and can solve practical problems very well." She also granted me the fellowship.
I want to go to those well-ranked engineering schools, like UIUC or Berkeley, and pursue a master's degree (and even a PHD, if possible). Although I do have a good research background, I'm worrying about my gpa. Most schools do have a gpa threshold, but is it possible for me to get into these schools? Thank you.

You can file for academic petition where university will initially reject your application but an academic committee will review it and may give you conditional admit. What happens in these cases is if you get more than 3.0 GPA in first sem , you are in the program permanently otherwise you are out.It may be better to speak with the department or program coordinator to get better understanding of this and they may have prior knowledge about these cases and may let you know if there is a good chance of your getting petition getting passed or not.
Alternately you can go to industry and work for couple of years before applying. An Industry experience definitely will add more value to your application and will show the committee that you are a serious candidate.

Grades are a factor but not the sole one.  There is always a possibility.  An option is to apply for a M.S. program first.  If you are able to get in and maintain good grades, you should be admitted into a Ph.D. program.


text:
import all references of a paper into a bibtex file
I have a paper that has say 100 references. I'd like to use a lot of them as references to a paper I'm writing, but it seems pretty laborious to go on each and everyone of them, search in google scholar and get the bibtex info.
Is there a tool available that given a paper\pdf\book etc, harvests all the references of that paper into a list or bibtex file?

This has been discussed on TeX.SE: How to automatically extract cited documents from pdf to .bib

The first option is to use a database that is mostly related to physics (I couldnt find there the paper I wanted), the other option is a tool that might be good but is not free...

This question sounds strange to me every time I read it. If you're writing a paper, you should include in your references only those sources you've actually accessed, read, and used, not just an arbitrary list of related references from someone else's paper.

There would be a quick approach if you know how to code:

Take the DOI of that publication.

Use that DOI to access the OpenCitations API. (Example here.)

From the API, extract all the DOIs that are referenced in the citing field.

Loop each referenced DOI through a DOI-to-BibTeX-converter (such as doi2bib in Python, or CrossCite)

Based on the great answer above, here's a tiny shell snippet that, given an input doi of a paper, will generate a .bib file containing the references of that paper.
export DOI="..." # put your input DOI here (not as a URL, just the DOI itself)
curl -X GET "https://opencitations.net/index/coci/api/v1/references/$DOI" | jq --raw-output ".[]|.cited" | doi2bib -i - -o "${DOI//[\/-]/_}-refs.bib"

To make this work, need to first install jq (available from any package manager, e.g. brew on macos) and doi2bib (available via pip).


text:
Reputation of 1 Year Master's in Comp. Sc. in the UK
I'm currently studying for my Bachelor's degree in Computer Science in Germany.
I've noticed that UK Master's programs, even at such prestigious universities as Oxford or Edinburgh, only offer 1 year Master's programs for full time study.
In Germany, on the other hand, Master's are usually 2 years / 4 semesters.
I was wondering how this is perceived in academia. Say for a professor in the US offering a PhD position, would he expect people from the German two-year program to be better at their subject? (Assuming grades are similar).

Are you looking at taught masters courses, or research ones?

Tendency is towards a taught one, but I'm also open to a research one.

In general, a student who has completed an MS thesis (as opposed to doing a course-work only MS) will be better prepared for PhD research.  Furthermore, the thesis itself is something that a potential PhD advisor can evaluate as evidence of the student's research ability.  MS degrees with course-work only are typically "terminal" master's degrees designed to prepare students for careers in industry rather than further study at the PhD level.

@BrianBorchers I did assume that all MS programs would require writing a thesis. At least for the one-year program in Edinburgh, these seems to be the case: http://www.inf.ed.ac.uk/student-services/teaching-organisation/taught-course-information/year-guides/taught-postgraduate-year-guide/degree-requirements


text:
Is it OK to let somebody know I refereed their paper?
It is not uncommon, especially for narrow fields, that you review papers authored by people that you might, at some point, come to interact with more or less closely. This can range from meeting them at a conference to even start a collaboration together.
Some times, when discussing with these people a point directly related to one of their papers it could be relevant to make a comment based on a discussion that came up as part of the reviewing process.
I have recently felt tempted to tell someone "hey, I refereed you paper, by the way, so I am particularly familiar with this and that..." but refrained myself because peer review is supposed to be anonymous.
Is it appropriate to bring up that I refereed somebody's paper when having a discussion with this person, in particular if it adds constructively to the discussion? Would it become "more appropriate" as time goes by and the review becomes "a thing of the past"?

Also related: Is it acceptable as referee to contact an author on a paper you review?, Are the referees of a journal allowed to reveal the title of the papers they review after the review process?

@NateEldredge Thanks for the links, I didn't find them while googling around.

No problem, I remembered a similar question had been asked before, but even so it took a little bit of work to find it.

but refrained myself because peer review is supposed to be anonymous.

Continue to refrain yourself. You can certainly say that you are familiar with the work of somebody else -- published articles can be read by anyone, after all -- but openly declaring that you were one of the reviewers would not add anything to the discussion and could put you in an awkward situation, if the authors haven't actually liked your review.
I work in a narrow field where almost all of the authors know each other and where it is not so difficult to guess who the reviewers are, also because journals ask the authors to suggest possible reviewers. These authors collaborate quite frequently, but I've never heard of anyone disclosing their role.


text:
How can taking a stance against for-profit journals hurt your career?
I will start by saying that I have nothing against any individual or company making a profit out of goods, services or intellectual property they produce. However, I do not like the fact that publishing houses, such as Elsevier (just to name the largest one), make a profit out of the voluntary/non-retributed work of others. By this, I refer to the fact that the core product these journals are selling are scientific articles written by others, based on research funded by others, and with a quality control (peer review) carried out by others with no cost to them. Then, research and academic organizations pay these publishers large amounts of money in the form of subscription fees to gain access to content the community provides for free.
Because of this, I have decided to, whenever possible, I will try to avoid submitting my articles to for-profit publishing houses and will try to rely as much as I can on the journals published by scientific societies. In my field (physics, materials science, chemistry) this is not necessarily a problem, since the APS, AIP, IoP, ACS, RSC, etc. publish a number of reputable journals that can suit my needs. I understand that other authors might not have a choice, or might simply choose to also publish with for-profit houses. This might force me to publish at a venue not of my liking when I coauthor a paper with people interested in sending the collaborative work to such venues. This is not a huge problem for me.
The case of peer review is more complicated, because refusing to review papers sent to me by a for-profit house does not only hurt the publishing house, but also the authors that submitted the paper, who are precisely the community whose interests I am attempting to protect by taking my overall stance against publishing corporations.
By submitting my work only to specific journals I am not actively engaging in any action that could be considered offensive by the for-profit journals and their editors. However, by refusing to review their papers I am directly saying "no" to the editor who sent me the work. I would like to know how I would be hurting my career by "soft boycotting" for-profit journals in the cases a) not submitting there, b) not agreeing to review their papers and c) both.

"Taking a stance" always has a price. Otherwise, it is a) meaningless b) no one else (but you) will notice. I do not think that anyone here can assure you how boycotting (including reviewing for) certain journals or publishers will impact your career. Probably it will do no harm, but who can tell?

I feel like this is a duplicate, but I'm on mobile and can't find it.

@guifa http://academia.stackexchange.com/questions/51938/what-are-some-examples-of-negative-effects-on-a-career-for-boycotting-elsevier-j and http://academia.stackexchange.com/questions/52224/is-reviewing-papers-mandatory seem relevant

If you don't publish in a journal you likely won't get asked to referee for it. Conferences may be a larger issue, since you don't choose were they publish.

@JonCuster "If you don't publish in a journal you likely won't get asked to referee for it."
If only!

@zibadawatimmy Thanks, those answer my question almost exactly.

@JonCuster Actually, the review request that motivated me to ask this came from a (reputable) journal where I have never published before.