text:
Someone asks me to cite their paper. Should I cite?
I submitted the preprint to arXiv and the manuscript to a Physical Review journal, and someone asked me to cite their article after seeing it from arXiv.
Their paper is a review. After reading that paper, I find that it has only a weak connection with our work.
My supervisor asks me to cite it. Should I refuse to cite?

Maybe your finding is not certain, and the connection is stronger than you think? You can ask your supervisor for more details about how it should be discussed and cited.

What reason did your supervisor give you to cite the paper?  ("Because I said so" is not a reason.)

I can think of a number of reasons to cite a source:

to acknowledge the work of others that you are building on (avoiding plagiarism)
to give credit to the author of a particular phrase that you quote (avoiding plagiarism)
to point readers to relevant previous literature
to signal that your work is at the cutting edge of the field, and
to situate your contribution in the context of related research
to provide evidence for a claim

"Being asked" is not among them.
Unless you retrospectively find that one of the reasons above applies (esp. 3-5), politely decline to cite the paper in question. In particular, you should refuse to add a citation as a favor.

Addendum: I just saw your update to the question, stating that your supervisor asks you to cite the apparently irrelevant paper. This complicates the issue. I would ask them to explain why and where to add the citation. Perhaps they want you to slightly revise your paper, incorporating information from the new source, which would justify the citation. If not, it depends on your relationship whether you are in a position to push back.

If the supervisor comes with a reason that can be fit under the 6 items listed in this answer: cite it. It's not worth fighting against if the reason isn't absolute garbage, unfortunately.

You can always ask for clarification on how the paper in question is relevant for you to cite.

I will just share my experiences (bad ones) to throw in some perspective.
I had submitted a paper once to a top conference in computer vision which was rejected for good reasons acceptable by me. But one of the reviewers, which I guessed was a top name in that area (also had a coursera course), asked me to cite 5 of his papers in the review. All were his papers.
A few years later, when I am doing my PhD, I got a paper accepted in a top conference. This time my supervisor sent me a list of 8-10 papers which I had to cite. Since there were constraints of space, he asked me to truncate a diagram and reduce the size of images to accommodate his list. Those papers had no relation whatsoever to my work. My supervisor is an IEEE fellow and has more than $1M in grants.
Citations improve H-index. H-index is crucial to get promotions and fundings. We had a very highly talented lecturer joining our university. He got 3 ICML papers accepted as first author (a top conference in machine learning) within a year, which is a fantastic achievement, but his grant application was rejected in favour of another lecturer who had 20 papers in mediocre conferences but a much better H-index. She works closely with my supervisor-- is a part of his nexus. The lecturer left my university and joined Google.
Academia is rotten with such practices. I regret that I agreed to add those citations - should have fought back. But then, fighting back is of little consequence when the system is fundamentally broken.

It sounds to me that someone needs to talk to the people issuing the grants. They have obviously adopted this procedure as a way of saving themselves effort. It is bad for academia as a whole and the problem needs to be rooted out. Maybe a prestigious general magazine would investigate and run the story. That would wake people up.  Corruption in academia is topical at the moment - at least as far as a well-known individual is concerned.

@chasly-reinstateMonica The nexus is deep-rooted. The academicians form networks even within the gran allocation committee. They form networks of reviewers and citations and reap rewards. For example, my supervisor connected to the editor of topmost IEEE transactions ensured that a paper is reviewed in a week to ensure the promotion of a colleague in my department. One could write a book on how rotten this whole system is.

Maybe these are the people to talk to. https://www.interpol.int/en/Crimes/Corruption

Corruption  in academia, especially in technical subjects could cost billions by promoting substandard work.

@chasly-reinstateMonica Please define substandard work and also clarify who will make this assessment?  The substandard work of one is perfectly fine for another.  Yes there is rot in academia, and yes granting agencies - sometimes for fear of being sued - avoid making qualitative judgments but on balance the system works reasonably well.  It is far from perfect and exceptions like the ones illustrated above happen all too frequently, but this kind of alliances always occur when too many people fight for decreasing resources.

@ ZeroTheHero - I was merely echoing what I inferred from the following passage in the above answer, "We had a very highly talented lecturer joining our university. He got 3 ICML papers accepted (a top conference in machine learning) within a year, which is a fantastic achievement, but his grant application was rejected in favour of another lecturer who had 20 papers in mediocre conference" - I took mediocre to mean substandard.

@chasly-reinstateMonica The problem of intellectual circularity is one that cannot be so easily solved: a good researcher is one recognized as good by other good researchers.   Thus the research landscape fragments into cliques (largely but not completely mutually exclusive) so that the work done by members of one clique is appreciated inside but not outside the clique.

@chasly-reinstateMonica  one needs to think long and hard before hitting a person in the career.  Such action must not be done casually.  Either you accuse somebody of academic misconduct, or you do not.  There is no middle ground, and serious ramifications.

@chasly-reinstateMonica I agree with you and I also endorse the use of the term substandard. at--ZeroTheHero A good researcher recognized as good by other good researcher is fundamentally a poor model and not suited for modern research. My university clearly sees these malpractices but continues to endorse it because it also brings it the money.  I wish I could elaborate more but for the character limit.

I'm honestly surprised, and quite sad, to see this as the last answer so far. I expected the first answer to be this. I'm just in the initial phase of my PhD, and pretty much from the very beginning have been seeing such disappointing practices. As a PhD student, my supervisor is not very happy with the fact that unlike many others, I don't write papers flooded with self citations of the works of our group. Unfortunately I have academic siblings here whose papers have been cited only by other papers of their own (many times) and those refereed by our supervisor, and it's deeply disappointing.

@nra I understand your predicament. It is a difficult trap to wade through.

So, basically Goodhart's law. When a certain metric starts to get used to decide policy, it will soon stop being a useful metric (as people start gaming it).

That's a horrible story. I guess Academia has too many people who game the system, but we don't know, from your anecdote, how prevalent these opportunistic strategies are. What is your suggestion for OP, by the way? Play along and cite, or don't?

@chasly-reinstateMonica citation boosting is an academic sin but neither illegal nor technically corruption. I don't think the police would be interested.

@henning--reinstateMonica I played along as it did not hurt me directly. The paper was already accepted and I was asked to make alterations for camera ready. After a few months, I felt annoyed about something similar. I raised this issue with the student affairs dean. And nothing happened. Confrontation is of little use. One has to wait for the opportune moment.

As terrible as this is, you make the same mistake by saying "He got 3 ICML papers accepted as first author". The prestige of a venue you publish in is an even worst measure than H-index. I'd take a well cited paper in a medicore venue over an uncited paper in a top venue every time. Neither is a substitute for directly examining the work itself though.

@IanSudbery Getting a paper accepted in a prestigious venue is one thing but 3 in the same year facing immense competition from across the world is a statement. And any university should strive to retain such a talent. As a PhD student, I am the one who lost most due to this. Getting to work with good colleagues is probably the most important thing in my career. Though at a high level your point makes sense.

Getting papers in three papers in a year is impressive, but it is the content of those papers that should be important, not the prestige of the venue. Otherwise this is just the same as judging people by the impact factors of the journals they publish in. Being accepted to a good conference/journal involves the judgement or 3, maybe 4 people. Being ctied 100 times involves the judgement of 100 people. Yes citations can be gamed - so can any system; so can journal/conference acceptance (we all know who our mates review for).

@IanSudbery Well, it is much easier to game the system to get citations than game three separate sets of reviewers for the 3 papers, in a double-blind reviewing system in the best conference in the field. Citations, many a time is inflated because a work, though mediocre, is easy to replicate, especially in CS. Master's students from not so good universities do that for their projects to churn out another mediocre paper while citing the original one. I would give more weight to a verdict of reviewers of the top conference than citations from such sources. No doubt, conferences are also gamed.

Should I refuse to cite?

Do nothing. You've read the paper and found it "has only a weak connection with ours," so there's no need to cite. You needn't refuse; just do nothing. If you must respond, then say something like:
Thank you for bringing your work to my attention. I have taken a look, but I don't see a strong connection and as such I believe it would be inappropriate to cite. If I've missed something, do let me know.
You can add a comma to the opening sentence and follow with I found it interesting, if appropriate.

I would limit myself to the first sentence.  The rest is just starting a debate that the OP will not win with a person so aggressively seeking citations and a supervisor suggesting to go along with the request.

Politics! Politics! Politics!

Citations are now (for better or worse) the coin of the realm.
It is inappropriate for someone to contact you asking for a citation.  This person can rightly bring his work to your attention but asking to cite is a spoonful too much.  You should be allowed to decide for yourself is this review is relevant or not to your work.
You and your co-authors should decide if this additional work is worth citing.  Those in favour should have an argument as to why this work was overlooked in the first place.
If possible, hold firm.   After all, you have (or should have) the final say as first author.

"It is inappropriate for someone to contact you asking for a citation." I disagree. A citation to a review yes, but I would absolutely not hesitate to contact an author if they failed to cite my previous work if they had done the same thing.

@ZeroTheHero I'd say it's fine to ask/tell if citing your work is neccessary for the "avoiding plagiarism" reasons (i.e. really should have been cited in the first place). Otherwise I agree with you.

My comment contained an error. It should have read: "It is inappropriate for someone to contact you asking for a citation." I disagree. A citation to a review yes, but I would absolutely not hesitate to contact an author if they failed to cite my previous work if I had done the same thing. That is, if their study was a address the same question as mine, particularly if it was using the same methods, then it should cite my study.

If you didn't read the review paper and went direct to the original paper(s), I can't see why you should cite a secondary source. If you did that exhaustively, you would include everyone's textbook about the subject plus the Wikipedia  entry!
Alternatively, if there is pressure, look for one or or more specifics where the reviewer has thrown light where you would or could have missed it. Or maybe give a cursory acknowledgement by simply saying, "There have been a number of useful review papers in this area including X, Y and Z."  and say no more.

On the other hand, if only read the Wikipedia summary of a paper, do cite the Wikipedia article rather than the paper itself! https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232290

This answer lacks some of the points that you made in your comments.


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Why don’t researchers publish their raw data for the advancement of science?
Publication bias. Reproducibility problem. Abusing statistical tests.
These are some of the many criticisms received by all fields of science for a long time. If I read an article on Psychological Science and am sceptical of their results, or if I want to apply another statistical techniques to see if the results remain convincing to me, I can't. I need to run another experiment. Or if I want to conduct a meta-analysis, maybe having other researcher's raw data is better than just the mean/CI they report in journals.
If scientists' mission is for public good and for the advancement of knowledge, why don't they publish their results in raw (of course they need to remove research participants' privacy information). They shouldn't be afraid of others' criticising their work. Only truth can endure the testing of time.
Nowadays, with the prevalence (and low price) of online storage platform and sophisticated database management, why don't they do it for the public's good?
EDIT: by raw data, I mean to make the dataset public and accessible to everyone (well... at least researchers)

What is the question? Researchers do publish the raw data. Often times they are not attached to the research paper. As no one wants to see a 500,000 observational table spanning 50 pages. Instead, they document their sources and methods such that you can reproduce it should you choose to. On this note, part of the review process is examining and dissecting the method itself to see if it is flawed.

The Square Kilometre Array telescope is forecast to produce 2 Petabytes of raw data a day. How does letting members of the public randomly browse that amount of meaningless (to them) numbers help with any of the problems you mentioned?

A few thoughts:

Publication bias

While making data available would help address some problems in publication bias, merely having data sitting on the internet somewhere isn't even close to enough to solve it if people still use journals as content curators.

Reproducibility problem

Available data = / = Reproducible data

I need to run another experiment

This is, in many ways, desirable. "I took the same data and got the same answer" is a fairly low form of reducibility. Yes, it catches statistical errors, and enables you to try new methods, but at least in my field, before something can really be thought of as "reproduced" it needs to be obtained via an entirely different experiment, preferably in a different population. That enables the understanding if there is a consistent effect that occurs in a variety of contexts, or if it was a fleeting result that was either noise, or (more philosophically) just the tail of an effect that is randomly but not perfectly distributed around 1.

Or if I want to conduct a meta-analysis, maybe having other
  researcher's raw data is better than just the mean/CI they report in
  journals.

It depends on the analysis you want to do, but this is not inherently true. Also note that it is often the case that, if this was what you're doing, an email to the researchers may provide what you need. Both times in my career where I have genuinely needed someone's raw data, I've been able to get it.

If scientists' mission is for public good and for the advancement of
  knowledge

You are making a massive assumption here: That the mission of scientists is the public good. A few notes:

Even for idealistic scientists, the actually doing of science doesn't occur in a vacuum. In order for you to continue to do your science, keep your people paid and the lights on, etc. you have to compete with other labs. Collecting data is often a long and laborious process, and there is a very real temptation to continue to mine that data past the initial publication. It is a competitive advantage, and science is competitive.
It is not axiomatically true that the public good from the release of data > the public good that comes from a lab being otherwise successful. An idealistic lab sacrificing themselves on the altar of data access doesn't necessarily help.

why don't they publish their results in raw (of course they need to
  remove research participants' privacy information).

This is a considerable hurdle. For example, there are a number of studies I've worked on where identifiable information is essential to the finding in question. This might be a special case, but it's not an uncommon one. There may also be agreements in place preventing this - many minority groups, for example, are very justifiably skeptical of "And then we can do anything with your data we want".

They shouldn't be afraid of others' criticising their work. Only truth
  can endure the testing of time.

Very often, the concern is much more about preserving the ability of their data to generate new publications over time.

Nowadays, with the prevalence (and low price) of online storage
  platform and sophisticated database management, why don't they do it
  for the public's good?

Because the public's good doesn't pay my postdoc's salary.
Now this all sounds jaded and bitter and horrible. Which is ironic, because I actually do try to make as much data as possible available to the public. But there are very real constraints, both on the nature of the data themselves and in the doing of science, that stand in the way of automatically making data available. One must be able to acknowledge these when thinking about data accessibility and reproducibility.
In my case, for example, what "the data" is is often a somewhat murky concept, and I find the tendency to view "I downloaded your code and data and ran it" as what people sometimes view as reproducibility to be...troubling.

Once upon a time, no data was published.
Today, large amounts of data is published, though in ways that preserve confidentiality of human subjects.
US Federal grants and contracts for most research now have a requirement that the investigators include a plan to make their original data available to users. One common way is to deposit the data in an archive managed by a large research organization. One example of this is the ICPSR (Interuniversity Consortium for Political and Social Research) Archive which is maintained at the University of Michigan's Institute for Social Research. Other universities have archives for their own research data.
The data is often modified to meet the standards of privacy required for federally sponsored human subjects. This usually means that some identifiers have been modified or removed. For example, age might be categorized in intervals of years rather than exact age. These modification are a condition of doing the research, so they can't be helped.
Federal survey data is mostly available on-line at the agency that collected the data, Census, Bureau of Labor Statistics, National Center for Health Statistics, etc. Some of it is free. Some kinds of data can be obtained if the requestor proves that they can insure the security data, such as patient data from the Center for Medicare and Medicaid Services. Federal agencies often have data centers where you can do your analyses and any requested results are examined by staff to insure that its release will not compromise privacy of respondents.
A vast amount of data is now published. The notion that an investigator owns their data and completely controls its release is dead, at least if someone else paid for its collection.
If you would like some data, contact the principal investigator or the funding agency and ask how to get it. At least in the US.

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writing letter of support for H1-B visa applicant
I can't find a suitable tag for my question. I hope I'm posting to the right place. I apologize if not.
I'm a prof in CS in US. I have been asked to write a letter of support for a graduate (BSc), call him X, who is applying for H1-B visa. The graduate is non-US and hence need the visa.
I myself have gone through the process several times many years ago. In all my experience, the hiring company has a manager who documents my performance and the letter is written by the manager with the support of the CTO, etc. As a software engineer (in a previous life), I of course totally understand the importance of CS education. But I also know that CS education alone without work experience is insufficient. That's why in all immigration lawyer websites I have seen, they always mention the letter of support should address the applicant's ability to actually perform their tasks. In all my H1-B visa application, my PhD advisor was never asked to write letters to support my H1-B visa application, whether it was for post-doc research, teaching or software engineering.
X has included in his email a webpage that say something to the effect that "Task A can best be done by someone with a CS degree" and wants me to use that too. As an educator, I cannot possibly vouch for whether X can perform his job or not. I believe I can only say something about his grades. Furthermore for all my students in the past 10 years, none of the surveys I have filled in ever ask "Can applicant do his job?". The questions are mostly about his skill level in comparison to others such as "Rank applicant 1-5 in terms of his programming skills." This is the same for all phone calls for reference checks. Also, X has not taken many classes with me.
Can anyone comment on this? This is a supporting letter for H1-B visa application, not for a job application. Thanks in advance.

I don't know how these work, so maybe I'm totally off base, but are you a prof in the US, or external to the US?

Sorry. In US. Should have mentioned. Will edit above. The letter is for a non-US student. Hence the need for the visa.

Having written something similar, I would go with available evidences.  In X's case, you can ask him/her to forward you his/her transcript and the subjects that relate to task A.  Then based on your expert opinion, given that X has passed these subjects, and the course X took is accredited, you can then say, as an expert and educator, you expect X has the required skills to carry out task A.  It is important to word your sentences based only on the evidences.  You cannot say X will complete task A, but you can certainly say he/she has the required skills.

In any case, if there is evidence of competence, it would come from his supervisor. Then clearly, as I mentioned above, the supervisor could have written the letter. I totally agree with you on real evidence of competency. This is not a general letter of recommendation to a company. This is a letter sent to INS. That means that I would have to verify the evidence, which means I would to talk to his supervisor anyway, which begs the question: why is his supervisor not writing the letter instead.

If you can only talk about his grades from a few classes, have you considered telling the person that you might not be the best choice for a letter of support?
Even just a class can be enough to see a student's skill, for example if a project is a big component in the class or if the instructor closely examines sufficiently detailed assignments and exams. This is really the useful kind of component: "X is skilled at task Y, as evidenced by his work doing Z..." If you just say someone is skilled without much evidence, it won't be afforded much weight anyhow.
If there has been no actual work, you can at most comment on:

Their grasp of technical knowledge taught in the course
Their intellectual ability (how quickly they were able to learn)
Their discipline and professionalism (e.g. in showing up to class, studying and submitting assignments on time)
Their talent for that for this area of work based on their performance in the course

It sounds like not much, so as I said, perhaps you might not be the best person to write this.
If you really want to write the letter, I would advise asking fellow faculty if they have experience in such a situation and whether they can help you.

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Is it normal to revise a manuscript a 4th time before it is published? Negative impact on my research?
I am a PhD scholar in mathematics, in particular number theory. Recently one of my research papers was published in a journal. This was the 4th revised version. All the 4 versions can be found in arxiv.  The previous 3 versions had some major mistakes. However I have made it accurate in the 4th revision making it vastly different than the previous 3 versions, and which finally passed through peer review process and is now published.
The one thing I am worried about: Suppose someone tracks that paper in arxiv and found that it had 4 versions before publication.
Would it make a negative impact on my research or it is normal in research ?

Isn't revision to a better version the whole point of doing math and science? The newer the idea you propose, the more mistakes you will make along the way. Don't ever feel shame or regret for "mistakes" of that nature.

For most of us, the risk of nobody ever reading the paper on arxiv is far higher than the risk of someone comparing the different versions on arxiv to spot the mistakes. That would be petty, and also a waste of time. I wouldn't worry about the revisions on the arxiv.

@Clumsycat. What are they going to do? Accuse you of learning and making progress?

Some very rough statistics using the number of results for a google search limited to "site:arxiv.org" with query "this version, v2" (with v2 replaced for other versions) v2: 234000, v3: 79400, v4: 24900, v5: 8040, v6: 2800 This doesn't work for "v1", but there seems to be around 4.5M submissions indexed by google. So, to the extent this approach is valid, from 2nd revision onwards there seems about a 1 in 3 chance for each next revision.

@MadPhysicist Your not wrong, but to be honest, some of my arxiv revisions do include quite embarrassing mistakes. Everything from writing Poison when I meant Poisson to mistakes in formula. However, if anyone is interested enough in my paper that they are checking previous revisions of it, then I'm more flattered than embarrassed.

Would you rather revise your manuscript until it seemed correct, or some certain number of times, whether it seemed correct or not?

@RobbieGoodwin, certainly the first option

It is not uncommon for manuscripts to change significantly during the review process --- this is what peer review is for! In my experience, having 4 rounds of review is a bit excessive --- typically most major errors should've been spotted pre-submission by the authors, or, when the main author is an early career researcher, by their supervisor. If major errors make it into the submitted version, it often leads to rejection of the manuscript, to encourage the authors to check their work rather than to lean on reviewers. If this is ensured, minor inaccuracies can be caught during the 1st and 2nd review.
Having said that, ultimately what matters is that you have successfully published a paper. You have surely learnt a lot about research through this process, which is the goal of your PhD project. Hopefully, your subsequent papers will be accepted easier and with fewer revision cycles. Good luck!

It would not make a negative impact on your research (how could be?) and it would not make a negative impact on your reputation.
From how you describe the work, however, it seems like you would need to find better collaborators, or to look for more internal reviews from peers, since 3 major mistakes in the same paper hints at the fact that the paper was not ready to go public in first place (in my opinion).
But then, arxiv may be used exactly for that, to have a blind peer review, so I do not see the issue with the history of your paper.

It's particularly difficult in a PhD because in "real life" it's easier to have collaborators with out impacting on the personal originality of the research.

I am also a PhD student in a number-theory adjacent field.
I don't think most people look at old arxiv versions except by mistake. There are many other reasons for there to be multiple versions. For example, one might revise the paper before submitting it to a journal, and then post an updated version to the arxiv with those changes, and then do the same to the refereed text (most journals allow this). There is also no particular shame in a young person posting mistakes to the arxiv, especially if they turn out to be salvageable as yours seem to have been. If these mistakes were caught by people reading the arxiv preprint, then the arxiv is doing one of its jobs. If you caught them yourself, it's probably a hint that in future, you should wait a bit longer to post things.

Thank you. Yes your first guess also happened. I myself found mistake and thereby reorganized the paper before submitting to journal. The journal published asked only one major revision. The other revisions are done before submitting to the journal

Would it make a negative impact on my research...(?)

Most/all answers say no. However in a competitive situation (be it healthy competition or nasty) it could still be brought up at some point - and when you might least expect it or be prepared to respond.
You might be giving a colloquium or a talk as part of an application for a position or funding, there will be questions, and someone may ask in a very polite way

Your results are fascinating! We can see from arXiv that your route getting there was equally fascinating, can you share some of that with us?

Have an answer in mind! Have a prepared response, so if the question ever arises, be it over tea or coffee or in a very exposed setting, you can respond without skipping a beat.
Make it an interesting story. Bring your listeners along for the ride. If it's necessary to mention a mistake, make the mistake sound interesting and delightful!
Everybody makes mistakes, but we often forget ours when thinking about others'. When you bring them along in your recounting it's more likely to remind them of their own (somewhat) similar experiences.
Do not volunteer this on your own. But have this ready if it ever does come up, no matter how likely.

...or it is normal in research?

It's not typical but what is/isn't "normal" isn't really a concern. I don't think it's a six-sigma event.
As other answers indicate, that part doesn't matter. There's no "normal" in research.

It's completely normal. Almost all manuscripts go through multiple rounds of revision (even rejection) before getting published; it's pretty much unheard of for a paper to get published as-is with no revision whatsoever. No reasonable academic would judge you poorly for having gone through revisions.


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Roadmap and possible pitfalls for a first-time software author to publish a paper on a Python package?
I'm not a software developer by trade but I am in the process of writing a Python package which models an experimental apparatus and physical process and generates simulated data. Results can be used to compare to measure data and extract physical parameters, or to predict how an apparatus will perform in order to modify or optimize it.
I'm aware of Github and Python Package Index and will make the software available through Github and hopefully PyPI though the latter may be a challenge for a first time package author.
I will then want to submit a paper for publication in an appropriate journal explaining the details (math and physics) of how the calculation works and demonstrate its agreement with measured data which would then refer to the software's source page(s).
Question: What kind of roadmap should I prepare for myself in order to do this smoothly and efficiently, and what are some likely pitfalls someone publishing software-papers for the first time may face?
I should note that there are one or two legacy packages that perform a somewhat similar set of functions, but they are roughly a decade old or more and available as compiled .exe files rather than open-source packages. I'm not using these or reverse-engineering them, but there will none-the-less be some overlapping in function.

different but somewhat related in that the answers and their links are instructive: Does building a Python library fall in the category of research? and also What is the threshold for a software paper to be publishable?

PyPI […] may be a challenge for a first time package author – Why? PyPI has not requirements for contributors AFAICT.

@Wrzlprmft because there is a review and there are several requirements that need to be met before they will accept a package https://packaging.python.org/tutorials/packaging-projects/ First time package authors may find this more of a challenge than those who have done it several times.

because there is a review – I fail to find any mention of this on the linked web page. In my experience (which is a few years old), packaging is a bit tedious, but not an insurmountable barrier.

@Wrzlprmft I'm confident that it "may be a challenge for a first time package author" is true as written. I never said anything about "an insurmountable barrier". I'm also pretty sure that humans review submitted packages before they are made available to the public on PyPL, as well as there being automated checks in place.

also related: Can open-source software be peer-reviewed and published? and linked there in Computational Science SE: Venues for publishing papers that emphasize software along with eleven answers!

I published a paper on a Python package myself.
Finding a journal
My main recommendation is to start looking for a journal now, even before you start writing.
Unless journals in your particular subfield of choice is very open to software papers, there are likely only a few journals you can choose from and those may have special requirements.
These requirements may not be obvious and if you do not fulfil them on your first submission, you may not get a second chance, which in turn is particularly bad if alternative journals are scarce.
Depending on the requirements, you may need to write your paper completely differently.
I would proceed as follows:

Find a journal whose target audience are potential users of your software.
Does the journal clearly state that it accepts software papers?
If yes, do they clearly state the requirements for acceptance?
Are there any precedents of software papers in the journal?
If yes, is any of them comparable to what you are going to do?
Comparable here less refers to what the software does, but on how it is “sold” and what the paper does beyond software.
For example, it could be that a software paper only got accepted through featuring new algorithms and yours may be rejected because it doesn’t.
When in doubt, contact the journal briefly outlining what your paper would contain and ask them whether they would consider publishing a paper of this kind.

In my case, the journal had a clearly stated policy for software papers and there was an existing paper for a competing software.
Still, I encountered problems with one of the reviewers recommending to reject the paper on account of being a technical manual.
Consult field experts
Going by your question, you may not belong to the typical target audience of your software.
If that is the case, try to solicit assistance from somebody in the target audience (if you do not have one at hand anyway), as to what they consider important in your kind of software or what they think about features of your software.
You do not want to focus on a part of your software that the majority of your target audience doesn’t care about.
Also, by all means let somebody from the field who has not used your software review your manuscript before you submit.
(There is even less need to worry about plagiarism here since you probably already published your software it this point.)
Writing process
Getting inspiration
There are many variants of software papers.
I have seen some without any code (despite the software being a code library) and those with a lot.
If the previous did not yield any clear recommendation in this respect, look for well-received software papers and let them inspire you.
(Beware that a crappy software paper may be well cited because the software is popular despite the paper.)
Examples
Whether with code or not, you are likely to feature some examples.
These usually only belong in one of the following categories:

Didactic examples that demonstrate how your software works.
I found it very helpful to choose these with extreme care.
For example, for me it was pretty clear that I needed five didactic examples that could not possibly be combined, but each of which could be chosen from a wide selection of use cases.
I optimised some of these cases to be as simple as possible.
I chose the remaining ones to exemplify other things as a side effect, so I would not need separate examples for these.
(On the other hand, you do not want to leave the impression that everything is a special case requiring tricks.)
Do not blindly take the examples from your documentation, because these are aiming at readers who are familiar with Python, have your software installed, and can directly test things.
Also, your target audience in the journal is different.
For example, it also includes professors who have last programmed twenty years ago in Fortran, but who may make some supervisee use your software.
Importantly, the reviewers belong in this category.
For instance, in my paper I took care not to use any advanced, non self-explaining features of Python in my examples, unless absolutely necessary (and Python is rather benign in this respect).
Impressing examples that demonstrate that your software is capable of handling particularly difficult cases, e.g., ones that no software before could handle or that are considerably better in your software.
It may also be cases that show that your software can actually further science by doing facilitating novel results.
It strongly depends on your software and the journal whether you need this, to what extent, and what to optimise for.
Either way, again this example should be carefully chosen.
If you show code in your paper, you also want to make sure that the example is not overly long.

Selling your software
Make it very clear why people should use your software as opposed to an existing one or doing everything by hand.
Do not forget that usability may be a relevant feature.
This is also crucial for the review process: You have to convince the reviewers and journal that your software is something the readers have to read about.
If the journal does not require a significance statement upon submission, consider to volunteer one anyway.

This is extremely helpful and exactly what I needed to read right now, thank you!

I've just asked Referencing a previously published technique or method, is it okay to cite the supplemental attachment? (advanced materials and surface science) and linked back here.


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Are there "gig economy" resources in academic research? Are they fundable?
In many fields of research, there are some tasks that are self-contained and could be done effectively by someone who is not a full time member of a research group, but has the required skill and background. The task may be time-sensitive but often everyone is already fully tasked.
One might call them part-time or contract or temporary post-docs.
There are plenty of situations I can think of where this might not work, or would be a bad idea, but perhaps there are cases where the benefits outweigh any potential academic risks. They might involve a side-project, or an early foray into a potentially interesting area where there is no current expertise or time for someone to start from zero even though things might not pan out.
Because this would not be an employee situation, work would have to be done off-site. It might involve reading, writing, searching, programming, thinking, checking for errors (grammatical, logical, arithmetic...), or other tasks that could be exchanged electronically, and where the results could be checked and confirmed afterward. (You wouldn't want you primary data analysis done for example by "someone on the internet"!)
However I've never really heard of such a thing except in special circumstances where the individual has a previous relationship with the research group, and even then it can be difficult to work out the proper monetary mechanisms with the university administration, or funding agencies. "Consultant fees" are not a common line-item in research proposals.
Are there situations where this is changing? Are there any examples of micro-grants to get small jobs done in non-standard ways such as this? Is there even some better vocabulary to use to describe this kind of arrangement than "gig-egonomy" jobs?

edit: Seeing some the comments below it struck me that this might not be a very popular concept among regular post-docs. I don't think this type of resource will ever put normal post-doc positions at significant risk. But here I'm just asking if it happens, how might it be funded, and what it might be called, not if it's a good idea.

In mathematics, you would simply find someone with the relevant expertise and invite them to collaborate with you on your project. It is considered perfectly polite to make such offers, and for the offeree to either accept or decline as she wishes. Pay wouldn't generally be expected; co-authorship certainly would be. I take it you are describing a research field where this is uncommon?

@Anonymous the tasks I've tried to outline are let's say orthogonal to collaborative work; tasks that might be routine, thankless, or have a higher than average probability of going nowhere. The kinds of tasks you wish you could just pay a small fee and have someone finish for you. It's not a traditional academic scenario, and may not ever be in widespread use, but it could come in handy. To be clear, I am not asking if it is a good idea or not, just does it happen, how it might be funded, and what it might be called.

Mathematics would be a particularly unusual field for something like this to be used due to the nature of the work, but an existence proof might be the use of an outside glass blower to make Carlo Séquin's Klein bottles shown in his Numberphile videos perhaps?

This sounds a bit like citizen science.

@astronat it really does not. Please read the question again, more carefully. What I've described is contribution at the technical level of a post-doc, but for a much shorter duration, and for tasks that can be done without an extended workplace presence.

"...reading, writing, searching, programming, thinking, checking for errors (...) or other tasks that could be exchanged electronically, and where the results could be checked and confirmed afterward." Is this not what the various Zooniverse projects do?

@astronat nope. That is not what individual "scientific citizen" contributors do for the zooniverse project. They do not do work at the level of a post-doc, nor do they receive pay-for-work. If you had re-read more carefully, you would have seen "They might involve a side-project, or an early foray into a potentially interesting area where there is no current expertise or time for someone to start from zero even though things might not pan out." and recognized the difference.

routine, thankless, or have a higher than average probability of going nowhere — Or in other words, research.

@JeffE indeed, but shorter, and without any of the (at least potential) perks.

Thanks for clarifying the comment after I replied. If you want postdoc level work to be done then I agree with Anonymous: find a postdoc to collaborate with, or just do the work yourself. Every job has its boring bits.

@uhoh I'm well aware. Please read my comment again- I've edited to make it easier to understand. By the way, a useful term for this could be "outsourcing".

@astronat thank you for your advice, but "To be clear, I am not asking if it is a good idea or not, just does it happen, how it might be funded, and what it might be called." And thanks for "outsourcing" but I'm holding out for something more contemporary.

You're describing student assistants.

@henning they would have to be particularly skilled and experienced students and also not students to fit my description fully, but I know what you mean.

I've seen this happen in a sort of temporary 'research assistant/intern' role. Normally there's data that needs to be crunched or transcriptions done and it works to have someone come in to do it whilst the main researchers are doing the actual analysis/research. These can be paid, but usually tend to be from a local university or similar.
For bigger projects, there are transcription and data services available online which can do large volumes of that sort of work for you, normally on a per page/per data set model.
I know you have explicitly said you don't want opinions on if it's a good idea, however I can't ever imagine many people wanting to farm parts of their research out to unknown people on the internet. The vast majority of research is sensitive either in terms of the raw data or in terms of the research goal. It would be too easy for someone to copy your work and beat you to the punch if you were working on something of interest. Therefore I can't really say how it might be funded or what it might be  called, because I can't imagine it actually coming into fruition

Thanks for your answer! I agree that there is a fear factor as well as some level of true risk in the general neighborhood of theft of ideas or research plans, and even if it were an exploratory idea, if it turned out to be interesting there would be the same fear on the part of the researcher and disappointment on the part of the 'contractor' of having to let something interesting go. Perhaps there is something fundamental in the structure of the research group that's evolved to accommodate the vagaries of human thought and behavior.

After considering this for a (very) long time (I really have in this case!) I've come to the conclusion that this is probably the right answer. There are too many human behavioral concerns for "gig" research contributions to catch on, except perhaps in unique, isolated situations. Thanks!

fyi I've just asked Have there been hiring and/or funding changes in academia allowing non-colocated research positions, full time, part-time or gig-like (lockdown)?

There are also privacy issues when it comes to research involving human subjects. Our data protection office, for example, doesn't allow third parties to transcribe interviews for us.

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


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Do academic journals ever recommend software writing tools for scientific writing that suggest better paragraph construction?
I'm working on some edits to a paper under review with coauthors. Comments include advice that a better writing style be used and awkward wording be fixed. Coauthors are comfortable and expressive in English as a second language but to me some sentence construction and phrasing is awkward and un-smooth and it sometimes takes me a while to see how sequential points connect. I'm not a particularly good writer myself.
Coauthors are readily amenable to grammar and word order fixes much but less so to paragraph rewrites; "no, that's now how I want to say it".
I sense that further suggested rewrites on my part might not be the way to go, but "objective" advice on writing might still be welcome.
Short of a professional technical writing service, are there dispassionate tools (e.g. websites or programs) that tackle paragraph-scale technical writing construction, and do academic journals every recommend any of these or similar? What other solutions might exist for this situation?

No, journals offer their paid editing services instead.

@AnonymousPhysicist yes indeed, see comment ;-)

I've found that answers to Co-author keeps rewriting the article in poor English are also extremely helpful to me!

Yes there are such tools. An example is Grammarly. Caveat: they won't be as good as having a real human proofread your manuscript.
Journals will probably not recommend any tool or service, unless they've formed a partnership with the tool/service (example).

This is interesting and aligns with what you say; I attended a talk at a university by some representatives of a (very) large academic publisher doing a "road show" giving general advice how to prepare manuscripts for their journals. During Q&A I asked them specifically about software tools to check grammar before submission, and was taken aback by the answer which was basically, "No, I don't know of any such thing, never heard of it." I was stunned at what I thought was incompetence at the time, but maybe it turns out that it's what they were supposed to say.

Universities often offer professional writing assistance. This can be courses, seminars, workshops or someone you can send your manuscript to for the exact purpose of proofreading and revisions.
Journals don’t generally offer such services to my knowledge (at least not in my field).


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What are the ins and outs of submitting two related papers that need to cite each other to the same or different journals? Potential pitfalls?
I'm currently in the middle of some calculations and modeling for two related but different papers on experimental and data analysis mathematical techniques, and have started drafting two papers.
Depending on how they fill out over the next few months they may or may not be best suited for the same journal.
Each paper and its readers will be best served if it references the other, and this may be in fact necessary to avoid having to have duplicate sections and trying to do extra work to make sure they are also sufficiently different that they are not copy/pastes of each other (i.e. avoidance of self-plagiarism?1).
The topics are sufficiently divergent that they really can not be combined into a single paper without it looking like two papers hastily duct-taped together.
Question: What are the ins and outs of submitting two related papers that need to cite each other to the same or different journals? Any potential pitfalls I should keep in mind?

1 Using same text in different papers sent same time? See also "Is there any reason why your papers can't cross-cite each other?" and "You can actually cross-cite papers that are 'work in progress', especially in initial submissions."

@Kimball I've already made it clear in the question that these may be submitted to different journals; voting to close and prevent answers moves to disallow anyone from comparing the two cases.

@Roland citations are supposed to work for the papers and for their readers, the way the papers are written shouldn't be subservient to the citations. While I agree the situation I've described is atypical, I have to question how "supposed to work" is defined.

Maybe your field is different, but in mine this is not so uncommon, and I think the main points to keep in mind are already addressed in the two linked questions.  If there is something else you're looking for, please clarify.  One issue I see is that your question is a bit open ended (are you asking about the submisison process?  writing process?  how to decide whether to submit them to the same venue)

@Kimball yes I see what you mean on all counts. I'll give it some thought, thanks!

Conferences and journals want contributions that are reasonably self-contained. This means, some duplicate paragraphs might be needed. You need to then cite the paper containing the duplicates, even if the duplicates are not exact. You might want to explain the other work, referring to it as under submission. There is nothing wrong with an introduction that explains (among all the other things that an introduction needs to explain) that the same model can be used for two very different applications.
It is hard and somewhat unfair to cite something that reviewers (and later readers) cannot access and that also might not be published at all or only appear after a long delay. Think about publishing a Technical Report or a preprint first for both articles, so that you can refer to the other one that way. If you are lucky, you might then update the mutual citation in both.

This is a very helpful answer! Starting with "reasonably self-contained" in mind for the benefit of the reviewers (as well as future readers) from the start makes it a lot easier to implement. There will be a software aspect and likely a Github link, that may serve the role of technical report if we don't opt for preprints.


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If an image is included in an abstract which is published at a conference, does that mean the conference must give permission if it's used in a paper?
I'm advising some students preparing abstracts proposing posters at an international conference.
I was just asked about putting images in the abstract that represent data. It's a photograph of a phosphorescent screen which we use as raw data for fitting, but it's certainly an image as well.
The image is not much more than thumbnail size and in a published paper would start from the original .bmp or .png and therefore be much larger, processed differently and carefully annotated.
The conference submission guidelines include this relevant bullet:

The Author agrees to and does hereby assign all rights, title and interest, including copyrights, in and to the abstract to the Publisher. When the abstract is ready for publication, it will be published at the Publisher's own expense, under the Publisher's name in a conference abstract.

I'm at a loss how to advise the students and today is the last day for submission (as usual).
This questions asks only about including or not including the image in the published abstract. I gather that the poster itself remains the property of the student and PI.

Different but potentially related:

What does assigning the copyright of a paper mean?
How to legally re-use images in paper and still continue to use and distribute them in slides?

Can you not contact the conference organizers and inquire abut the issue? Maybe it is less of a problem than you think

@Sursula-they- ideally yes but it's Friday afternoon "...and today is the last day for submission (as usual)." So I'm trying to provide the best guidance I can find. :-)

Do not give away the copyrights of images that you would like to publish in a paper, unless you think that the image will be an outstanding contribution to your poster (it looks like it does not).
Giving away the rights to something is not intrinsically bad (depending on your ethics/moral conventions), but you will need to spend an additional 5 minutes in the future whenever you want to reuse that image (you will always need to check with the publisher, it is 99% sure they will let you use it for free if you use it in a research/academic context  ...).

In the specific situation described in the question, would the student actually be giving away the copyrights of the original image - i.e. the raw data?

I have no idea about the underlying data. Ask a professional. An example of the legal implications in the US:
https://deepblue.lib.umich.edu/bitstream/handle/2027.42/83329/copyrightability_of_tables_charts_and_graphs.pdf

Based on that the answer to my question seems to be a pretty clear "no", and that's how I'll proceed. Would you consider including it in your answer? I think readers will find it extremely helpful!

Unfortunately I cannot vouch for the content of that document, I did not double check that the references therein are true and valid. But since I think it can be somehow a starting point to investigate the issue, I leave it here in the comment.

Note that copyright covers expression, not ideas (nearly everywhere, but laws differ). It is tha specific image that you would give up copyright to, not the underlying data. And not to a different image based on that data. But, it needs to be sufficiently different. I'm surprised, though, that a publisher would care about copyright of posters.
Moreover, when you give up copyright to a publisher you normally get back a license for certain uses. Those uses might not include the right to republication other than in a dissertation. You need to investigate and understand that license, since it gives you some rights, but not all rights. And, if necessary, you can ask the publisher for a more generous license.

Note also that a copyright owner controls publication of "derived works", hence the requirement that a new image be "sufficiently different". A bit subtle, of course. But (most jurisdictions) copyright is a civil law matter so it is up to the copyright owner to complain. One basis of complaint is that the infringing work reduces the "value" of the original, which seems unlikely here, though not impossible to imagine.


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A friend helped me with a presentation – plagiarism or not?
My friend helped me with my assignment. I was having a bit of trouble and he showed me what he did.
The assignment was a speech with a powerpoint in the background.
I did not receive any help in the speech and it was all my own work but two of my slides are similar to his, and I copied his table. The speech is the part directly getting assessed while the powerpoint is merely for the theatrics. This was all done with his permission and he himself showed me how he did the slides.
The powerpoint was twelve slides long. Does this constitute plagiarism?
Edit: I did cite him in a bibliography which I submitted for his contribution. I, however, did not cite him in the PowerPoint. Also, the similar slides are not in the PowerPoint anymore but the table still is.
Edit 2: I was not found guilty of plagiarism, however, I did lose 10% due to academic misconduct.

Is the theatrics evaluated in your grade?

This is what I tell my students: https://www.cs.umb.edu/~eb/honesty/ . I'd approve of your getting help, as long as you acknowledged it.

Could you expand on what you mean by 'copied his table', and what this table contains? Did you literally copy and paste it into your own slide deck? Or did you use the same row and column labels, or other formatting? Did you perhaps just use the same PowerPoint table presets? Was the contents of the table something you have no flexibility in reporting, such as raw data?

Sometimes I am really surprised by questions and answers. I can give you an entire presentation. It might be unfair to the teacher, perhaps you are not learning, and other dozen - bad or not - things. But forget plagiarism.

My friend helped me with my assignment...I copied his table...does this constitute plagiarism?

Yes: You copied his work, doing so without attribution is plagiarism.

But if you put a notation at the bottom: "Table from " then it is not plagiarism.

@GEdgar what's the betting there was no mention...

The certainty exuded by this and other answers bothers me. "Helping" is not plagiarism, and we have no idea what was in this "copied" table or "similar" slides. Certainly I am concerned (particularly if OP asks the question because their teacher is accusing them of plagiarism), but I do not believe we have enough information to say that this is (or is not) plagiarism.

@cag51 I copied his table is plagiarism to me, when done without attribution. I agree that plagiarism cases are nuanced, but, outright copying a table, seems like a clear case of plagiarism. That said, perhaps elaborate on your perspective in an answer.

I think Matt's comment on the question is dead on -- any answer I could give based on the current facts would be very wishy-washy.

Whether it is plagiarism or not, and it is, may be less important than the bigger issue that it is almost certainly academic misconduct. Only your professor can give you advice on whether it is acceptable.
Getting some help may be fine, depending on the rules. Copying a table is less fine and becomes plagiarism if done without attribution. I would disallow it if I learn of it and would encourage you to do better. Since you are a student, I would even discourage your use of "similar" slides since you learn more by working independently and that is the point of the exercise.
The proportion of the copying makes no difference. I assume that you didn't reference your friend in the slide deck, making it plagiarism. I suspect that you think it is probably wrong to do this if you didn't cite the work of your friend.
Don't lose track of the lesson that learning is the real objective, not the production of any artifact.

+1 for "Don't lose track of the lesson that learning is the real objective, not the production of any artifact"

"The proportion of the copying makes no difference" - doesn't this lead to the heap paradox? Even with no copying, there will be at least a few words which will be the same. And if not that, then certainly some letters. If I've already seen "i++;" in someone else's program, am I forever forbidden to use it in my code? If not, then what is the smallest amount which is still fine?

@vsz It's the process of copying (and representing as own result) that makes plagiarism, not the amount of it. If you by chance come up with the same combination of words as someone else, it's not plagiarism. If you report even a single number you knowingly took from somewhere else, and you don't cite, it's plagiarism.

Regarding your "i++" example, it is indeed copying, but as now one will assume that you came up with that on your own, and you don't explicitly claim that this is your fancy new idea, it's not plagiarism.

This is definitely not plagiarism. It's like saying you copied Microsoft's works for using PowerPoint to do your presentation. Both Microsoft and your friend created an environment for you to do your works. You don't have to give them any credit.
Your friend didn't do the works for you. You did all of it yourself.

I think this answer is incorrect. The OP's friend created the slides that was used in the OP's presentation, i.e. "your friend did do the works for you".

@Allure Microsoft created the software that used in the presentation. Did Microsoft do the works? Had you ever credit Bill Gates on your presentation? Microsoft did do the works.

I don't understand you. Microsoft created the program which OP's friend used to create the slides, and it's the slides that were used by the OP.

@Allure Thus, the slides by OP came from help with Microsoft and the friend. We don't credit Microsoft, so why should we credit the friend? If we don't need to credit the friend, why is this a fraud? Remember, OP only used the template from the friend.

@SmallChess If that bothers you, you can see it as a matter of expectations. Your teacher expects you to write the content of your slides. Your teacher expects you to use off-the-shelf office software. Not communicating that you used someone else's source material (e.g. tables) in your slides is deceptive because then people would assume that it's all your work. Not referencing Microsoft is accepted, because your teacher doesn't think you wrote your own software anyway.

@SmallChess if you think that way, what could possibly be plagiarism? I could turn in my friend's assignment and say, my friend created that assignment using Microsoft Word, and since we don't credit Microsoft, I don't have to credit my friend either.

@Allure Plagiarism is about someone else doing the works. Neither Microsoft nor the friend filled in the slides. It is 100% original works. OP did everything, perfectly legal. No plagiarism.

The OP does not claim to have created PowerPoint, but can be assumed to have licensed its usage. However, by presenting the slides the OP does claim or imply to have created the slides.


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B.S. in Electrical Engineering a "Professional Degree"?
You always see those education checkboxes where you pick your level of education; i.e. you have high school diploma, some college, associate, bachelor's, masters/professional, then finally doctorate/professional. Would you check bachelors, masters/professional, or even be able to check doctorate/professional, if it is technically a professional degree? I know this is really more of a technicality, but I'm sure it's best to mark yourself as high as you can.

A better term might be "graduate degree." But in this context, "professional degree" would mean "higher than bachelor's."
The main "professional degrees" used to be MD (medical doctor), JD (Juris Doctor or lawyer), and PhD. Later, MBA (Master of Business Adminstration) became popular. So "other"msasters, M.S's or M.A's, could also be "professional degrees."
Yes, B.S. of Electrical Engineering would be a professional degree in the literal sense of the word. But not in the above sense.

Of course I appreciate the answer, but I must ask, would a master's degree in Electrical Engineering then be a professional degree in the above sense? Professional Engineers are licensed and are definitely more suited to the above meaning of having a professional degree than someone with an MBA.

@RoryHector: Yes, an M.S. in EE is the equivalent (or better) of an MBA in this regard, and are included in "other"  masters (e.g.M.S.) degrees.


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Does a senior area editor supervise a country or a region?
What area is being referred to in the title senior area editor? Is it a country or a region that may include more than one country?

It is more likely to mean a subfield of a larger field. Someone responsible for papers on, say, Algebra, at a math journal. "Area of expertise".

Thank you. It now seems that this question would've been more appropriate in
elu!

Most journals accept papers from a fairly large spectrum within some field. Most of the time the field contains specialties that require deep knowledge. No person can be expected to be expert in all of those sub fields. Therefore, a journal's editorial staff is likely to contain people with at least some knowledge of a specific subfield. For a math journal there may be "area editors" for Algebra, and Analysis, and such. Perhaps even sub-sub fields within those fields.
So "area" here refers to area of expertise, not a geographical designation. (Possibly different in a journal devoted to geography, I suppose.)
But even here, the specific knowledge of an editor is limited, hence the assignment to reviewers who are expected to be much more knowledgeable in the specific of a given paper. The area expert (editor) can do a rough estimation of the quality and suitability of a paper, but it requires deeper analysis.
A journal that published in various languages, of course, would need people to sort those, but that isn't the main idea behind the term.


text:
How to proceed when one peer reviewer gives a much lower score than the others but provides no negative feedback?
I have received peer reviews for an academic proposal for a project. Three reviewers (A,B and C) submitted sets of observations and scores for three criteria/sections of the evaluation.
Reviewers A and B gave generally favourably worded reviews with pertinent clarification questions and observations that reflect themselves in the scoring they awarded for each section - generally high, with explanations on why deductions were made.
Reviewer C gave significantly lower scores for all sections when compared to A&B but their review only mentioned positive aspects of the project proposal and no questions or negative observations.
For each criterion I am able (and expected) to submit a short "applicant's rebuttal" in order to offer answers and clarifications which address the reviews for that section (one combined field for all three reviewers per section). The three reviewers are going to see these observations, have a panel discussion and potentially amend their scores/reviews if they see fit.
Would it be appropriate to politely point out the discrepancy between A&B's and C's scores and note that much higher score deductions were made by C without any suggestion on what could be improved, taking into account that I would have to do this for each of the three sections in the evaluation?
Should I instead just focus on answering A&B's questions and hope that C would (if their score deductions were concerning the same questions) favourably change their score?
Any suggestions on other ways I could proceed with this situation would be greatly appreciated.

My suggestion would be to ignore the scores and focus on the comments. For any comments from anyone that are positive, thank them. For any comments that are negative say how you intend to address them to make the project better.
Fighting over the scores is a matter of interpretation. Ignoring C's positive comments leaves out an opportunity.
Don't think of it as a "rebuttal" but as a "response". Focus on the positive aspects whenever possible and on how you can address any others. Leave the interpretation for others as they will do their own interpretation in any case.
Perhaps C is just known for this.


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Not grammatically strong
I am an undergraduate student from India. English is my third language and I am not grammatically sound in it. How bad could it be for my career (in academia) and how can I improve on it.

Who else in the world is not in your situation (or even worse)?

@Alchimista: Native speakers of English.

@Wrzlprmft From what can be read across the Internet, and sometimes even here, I'm not sure about that ;-)

Like anything that you need to learn, the key is practice. Reading alone won't make you a better writer. You need to write. Moreover, you need to get feedback on your writing. Of course, if you submit a paper and it is sound but uses poor English, the reviewers will often try to help, but their patience is limited. So, in some way, poor skills in the language of expression can hold you back until you improve.
I assume that you are also in a place in which it is easy to use your first and second languages, so English may not be in everyday use in your circle. But if you are in India, for example, there are plenty of competent English speakers around you. You can try to associate with them to improve your speaking skills. You can also, perhaps, find or create a small group of people to work together on improving your writing skills, giving feedback to one another. The writing needn't be scientific writing, actually. Anything will do to start. But in such a group you should all force yourselves to use English nearly always. The only exception would be to provide definitions of uncommon terms.
You can probably also find local classes in English as a Second Language (ESL) which offers help both in speaking and writing. The local secondary school might be able to help, for example.
Practice, practice, practice. Get feedback. Practice some more. Getting feedback is probably the harder part of the problem.

Clearly it's a big advantage to be comfortable at writing in English to work in academia. If you really struggle with it, it's definitely worth investing your time to improve your level. The good news is that you're not the only one (the vast majority of people in academia are not native English speakers either). Don't worry, it will improve naturally by reading and writing papers.
you can find a few ideas how to improve here. My personal advice is to read multiple times the papers/authors that you like, and make note of the phrasings that you could reuse later.

English importance:
Poor English is tolerated a lot in science/engineering (compare for instance to marketing).  I would argue too much but this becomes very touchy.  In any case, you should just worry about YOU, not the system.
Bottom line in math/science, it will not be a major hurdle.  Furthermore in general (in general, not every instance, caveat, caveat), Indians have better English than a certain other large population Asian country. So.  You might have some protective cover.
All that said, English is the language of the world, of academia and of science/engineering.  It's the lingua franca.  (Now the French are mad at me.)  Having a better facility in English will help you interact, attract grants, tell jokes, make connections, etc.  It's not the end of the world.  But it is helpful to want to get better. You have the right impulse here.
How to get better:
The key way to get better in a language is TO PUT YOURSELF OUT THERE.  Talk, drink, ask gi...people out.  Just converse.  Readily and openly and making mistakes as you go.  You will get way better, way faster, and have more fun along the way. DON'T hold back because of worries about grammar but just plunge along bravely.  I have learned this in several foreign languages, including in intelligence work in country.  GET INVOLVED.  [None of this is to say not to study the language and do formal instruction...you can/should do that ALSO.  But you must get involved, immersed, and bravely.]


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What are the stages for pursuing medical sciences in America
I am not an American citizen but wish to pursue my degree in America. I am currently enrolled in a bachelor's program and I am expected to graduate in 2020. Do I need do a master's program in America to pursue PhD ? Or there is direct enrollment ? (In my country the understanding is first you do a bachelors then a masters and then pursue PhD. My area of interest is Virology.

What do the institutions, who have the program(s) you want, offer?

So I was just surfing web on elite American colleges. I found that almost all of them offered PhD and not Masters.  It talked of GRE and TOEFL scores

For example Harvard

So what do you expect now?  Decide which one you want and make sure you meet the requirements...

It's important to distinguish between MD programs (that qualify you to be a physician), PhD programs (that qualify you for research but not the practice of medicine and make it difficult to do some research that involves interaction with patients), and MD/PhD programs that qualify you for both roles and for research directly involving patients.

For a student in the U.S. system, the common academic route to PhD admission in biomedical sciences is to obtain a bachelors degree and then to apply directly for PhD programs. For competitive programs, research experience is very important for applications, and so many applicants do additional research in between their bachelors degree and PhD applications: working in academic labs, participating in post-baccalaureate programs, or sometimes participating in a program that offers a masters degree (particularly if you are taking a more interdisciplinary route), but the masters degree is not usually a strict requirement for a PhD program in biomedical sciences.
Masters degrees are uncommon as a goal in biomedical sciences, and many institutions do not even offer them as a program that accepts applicants. Instead, masters degrees are sometimes awarded to PhD candidates who choose to end their studies early, or they consist of add-on programs (almost like a more developed 'minor') meant to accompany a PhD and are applied for simultaneously. Of course this can vary with the exact institution, and varies in other fields.
For a student outside the U.S. system, things can be more complicated. As discussed in the comments by BrianBorchers, U.S. institutions vary in how they treat bachelors degrees completed in other countries. A 3 year program (an actual 3 year program, not a 4 year program completed early) may not qualify. In that case, your best option may be to get a masters degree in the educational system you got your bachelors degree in, but this is something you should discuss with individual programs you may be interested in applying to in order to find out their specific rules: there is no guideline that will apply to every school or every program. Alternatively, programs may instead have a course of study in mind that you will have to have completed before your application is considered: it will be more important that you can show you have completed those courses in your studies rather than the specific length of your degree.
Most major PhD programs in the U.S. are going to have a web presence with rules and admissions requirements posted, as well as support staff for the program. You should read these as thoroughly as you can, and then ask additional questions to the staff.

You want to be a researcher and not a physician?  Yes, there may be direct enrollment for bachelor's degree recipients into Ph.D. programs.  When you begin in your final year, check the web pages for Ph.D. programs of interest to you to see what the requirements are.

I wish to pursue a career in development of anti viral therapeutics but not actually work with the patients themselves. Is it true that in America you need to have 4 years bachelors ?

There's a separate question about whether a 3-year bachelor's degree is sufficient to get into graduate programs in the US.  Some programs require a 4-year bachelor's or a master's degree and won't accept a 3-year bachelor's degree.

@BrianBorchers What is even the difference? I did a 4-year degree in three years. Where are there programs defined as 3-year?

I'm not trying to defend the practice, just saying that some universities in the US treat 3 year bachelors degrees from countries like the UK and India that have 3 year bachelor's degrees as not equivalent to a 4-year bachelors degree from a US institution and require students to have another year of higher education (e.g. a UK honors year or a master's degree) before admission to their graduate programs.

My bachelor's degree is 3 year program. What kind of 1 year course could I do ?

Is there concept of masters in USA ? what are the qualifications generally scientists have ?


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In research proposals, why do investigators need to claim a certain fraction of their salaries, from the proposed budget?
In research proposals, why do investigators, who usually are permanent faculty members, need to claim a certain fraction of their full-time salaries, from the proposed budget? Are they not paid in full by the university?

There are several reasons in the US. Most faculty are paid for 9 months of the year not 12. They may choose to spread out their pay into 12 payments a year, but their base salary is for 9 months. Grant funding is one way to supplement their pay up to a full 12 months. Unfortunately, the National Science Foundation, which funds a lot of academic research in the US, only allows a maximum of 2 months to come from NSF, so professors must diversify somehow as well.
Additionally, some faculty may choose to buy out some of their required teaching. Many departments will allow you to teach less if you can bring in even more of your salary. Sometimes this is done with grant funding, but I think more often it is done using endowed chairs.

In regard to the questIon, a 9 month salary means essentially that faculty are not paid in full by the university, but only paid 75%.

@StrongBad Rather, faculty are paid fully for the work they do during 9 months of the year and are free to do other work (or no work at all) during the other 3 months of the year.

@StrongBad, I would say "sort of". Generally all the money a professor receives will come from the university, but they start out with a number that represents 9/12ths of what the professor could be paid. If the professor wins some grants, they can fill in up to 3 more 12ths at their current monthly rate, but the checks keep coming from the university. If the professor decides to do so, they may generally seek outside employment during the summer months rather than grant funding, and that money would come from someone else at a rate negotiated separately.

Does the same apply in the UK?

I'm not aware of anywhere outside of the US where 9 month faculty contracts are used.

In the UK at least, it is because the funder is contracting with the university for their employee's time. This PowerPoint from Birkbeck, for instance goes into costs etc, plus the requirement for institutional sign-offs. The investigator will continue to be paid by their university as before (normally) but the University will be compensated for the relevant time.

So the investigator's salary remains unchanged, but the university gets an extra income?

Yup. I mean, scholars with a track record of successful grant applications are more likely to get promoted or move on to better jobs or go up the professorial scale if that's where they are in the hierarchy, but they don't get a cut of the grant directly (beyond say having access to a grant-linked conference travel budget etc).

I see. So they get promoted because of that extra income they bring for the university.

@adipro It's generally not profit to the university. The income is typically used to keep the lights on, maintain buildings and libraries, and pay for admins. These are usually known as indirect costs. In the US, these are pre-negotiated at rates with the federal that add a percentage to the total direct costs (salaries, etc) of the proposal (about 56% at my university). UK agencies appear to pay up to 80% of these costs. It doesn't turn into profit for the university at all. Unis like this money, but it buys them flexibility not champagne parties.

@adipro On your question, well they are more likely to get promoted, because they are bringing in the reputational and financial benefits of the grant income, but nothing is certain.

Otherwise, as @BillBarth quite correctly says, this isn't profit for the uni. It covers a proportion of the overhead - a relatively high proportion in the case of the UK's funding councils.

This varies by the industry, as well.  Many NIH funded researchers in the biological and health sciences are effectively full time researchers, and their salaries are not funded by their institutions directly (rather, are often 'paid' in laboratory space).  NIH grants pay their full salary (up to the NIH Salary Cap, linked to here for 2015).
Institutions might give these professors a constant salary from the institution, with the expectation that most/all of that salary is reimbursed through grant work.  (Ignoring tenure, for the moment; of course a tenured professor may receive a salary even if they are unable to find sufficient grant work for an extended period of time.)


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IT, life sciences and self-hate
To give you some background: I spent 4 years getting a PhD in a second-tier university in Europe, struggling heavily with no input, mentorship or encouragement from the PI. Then I did 3 year of postdoc-ing in even lover-tier university in Canada, which I had to quit, because I wasn't able to sustain myself any longer on poverty-level wage. It is over 7 years, plus undergrad and M.Sc. before that.
Today I browsed through job ads for programmers on StackExchange. Wow! Just wow! I wasn't able to handle it. I was really ashamed of myself. There are jobs with 6-figure compensations, there are companies that pay your relocation and sponsor your visa!!! There opportunities to work remotely, there opportunities in interesting places like Tokyo! I am thinking that even if I didn't have brains to become a Senior Dev with decent salary (not everyone has the talent!), but at least I would have FREEDOM -- I could change my job, if I didn't like it (like most of normal people). Only if I had chosen the right path years ago.
For someone with a "life science" PhD there only "cookie-cutter" postdoc openings from NatureJobs with crappy salary and guaranteed 60 to 80 hr workweeks with no raises and overtime. On top of that, I am often advised to scrap that PhD off my resume altogether, to increase my "employability".
It is really tough on days like this! I keep asking myself "Why? Why did I do this myself?" Am I really such an idiot? Have I been lied to? Have I been blind? Why in the world did I spend 7 years of my life on useless crap that drags me down? Am I the worst person in the world? I cannot imagine what I could have achieved if I spent as much effort while learning to code, as I spent doing all those useless experiments?
I really cannot stop blaming and hating myself! I have botched my life by trying the academic route. Sometimes I do not know whether it is even worth living further as this life science PhD will keep destroying me till the end of my days.

Voting to close because this is not a question. But changing from a scientific discipline to IT is totally possible.

What's the problem? You just said yourself there are many great opportunities just in front of you! Way to get out of a career dead-end!

"I really cannot stop blaming and hating myself" I recommend that you work on this mindset, which is not conducive to health or happiness in the long run. Please speak to a mental health professional, or even a friend or family member as soon as possible if you are seriously questioning whether it's worth continuing to live.

"Good" fields come and go. It is not that long ago that the dotcom bubble burst, and being a programmer was the worst choice you could ever have made... Similarly, the COVID crisis may lead to a "golden age of life sciences". Who knows?
Trying to find the field that will be "the future" when you are done is extremely hard because of just the impossibility of predicting future technological development and because of the pork cycle (Very briefly: you can choose a field for which there is a high demand now, but your fellow students know that to and will also choose that field, so by the time you are done there is an oversupply of candidates...) So don't be too hard on yourself.
If you really want to retrain, then that is certainly possible. People I know who work in tech companies tell me that most of their programmers are not originally trained as programmers or computer scientists.


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Have there been hiring and/or funding changes in academia allowing non-colocated research positions, full time, part-time or gig-like (lockdown)?
Almost four years ago I asked Are there "gig economy" resources in academic research? Are they fundable?. Now that much of the world and its academe has endured pandemic and lock-down, I wonder if things have changed in terms of research.
Question: Have there been any hiring practice shifts in academia which allow for non-colocated research positions, either full time or part-time? In other words, the worker remains in one location (e.g. city, country) but is hired to participate in a research group associated with a different location. These might include some kind of "adjunct research position" (if such a construct is possible) , postdoctoral positions or even, yes gig-economy-like contracts to participate in research.
It may be too soon for any wide-scale surveys of such changes to have been done or documented, so if there is evidence of a significant change in one or more large research institutions (e.g. a university), or a policy update in a funding institution that would be enough for an answer for the purposes of this question.

I think we are probably not far enough out of 'lockdown' for things to be clear yet. I am aware of various instances of this, for example where people have started a new job but not (yet) been able to physically relocate. At present, I think there is a general presumption that they will move 'at some point', and nobody has confronted the issue of whether this could become a permanent arrangement.

Note that working from a different country generally carries all sorts of tax/employment law implications, and so it seems unlikely this will become an officially-sanctioned mode of work any time soon.

@avid yes, if it's within some geographic constraints where conditions of employment are agnostic, then it's not as challenging, but if the person were in a different country and wanted to make use of say health insurance there could be problems if that ended up being travelers insurance. I'm just thinking out loud here, I don't know exactly how that applies, but its why I included "gig-economy-like contracts"

I think it goes deeper than that - if a university in country A employs you and says that your place of work is in country B, then your employment is likely subject to the employment laws (minimum wage, safety compliance, grievance procedures...) and tax rules of country B. (If this weren't true, dodgy employers would channel all employment contracts through some country with minimal workers' rights.) Compliance becomes a major headache and legal risk.

@avid yes I see, so I've asked for examples of changes rather than "What are potential problems with X?" in order to flush out ways in which these problems might have been addressed or somehow creatively avoided. The pandemic is  "work in progress"...

Let's be clear.  You are talking about a position that does research, but has no teaching?

@GEdgar Yes, I've modified the "adjunct" bit to as not to suggest teaching.Thanks!

In my university the emphasis is now on the transition back into the university. This is more complicated then expected, so there is no capacity left for developing new arrangements. So now there are lots of ad hoc arrangements that are expected to be temporary, but there has been no change in the main arrangements. I would expect that it will take a long time before that changes; the backlog is just too big.

I'll focus on the "gig" aspect primarily.
I doubt that this will occur and sincerely hope that it doesn't. The problem is that the gig economy is explicitly exploitive of its workers. It is designed that way, actually.
Those who try to make a living as an adjunct (most commonly in teaching courses), need to juggle around five different positions in order to make a minimal living. The pay is incredibly low in the US and there are no guaranteed benefits for part time workers. No health coverage. No pension. No say in university policies unless there is a union.
Some people teach as adjuncts because they already have a highly paid position elsewhere and just want some connection to students and faculty. For them, the money (or lack of it) means nothing. Some of them might get involved in research with other faculty, but don't depend on that for income. It is a hobby in some sense, though I know people who do it well. The "win" for them is in the connections, nothing more.
To try to extend this to a research career, juggling several gigs, seems impossible. The problem, at base, is that it is difficult to do real research on a part time basis. If you are working on a problem (I'm thinking math, actually), you don't normally turn off your brain to move on to the next gig after the two hours you've allocated to this gig. So, you wind up self-exploiting if you really do the research right and the employer is probably counting on that.
There are some positions that might be available in grant funded existing labs, especially for specialists. These are more likely to be short term, rather than part time, I'd think. Hired for a particular task within a larger one. But that has always been a possibility. And there is no possibility it can be done remotely in many fields.

To expand to the other aspects of the question, not that in some fields you don't need to be co-located to do research together. Many of my papers are with widely separated (several continents) colleagues. What is needed is the ability to communicate and that is possible now. But my university wouldn't have been willing to hire any of my co authors unless they moved to this location. One of the reasons has to do with law. But the bigger issue is that a university has a diverse mission. Even R1 universities have a teaching mission, including undergraduate in almost all cases. That is much harder to arrange remotely and still fulfill all employment regulations. And again, it is a special problem for part time work (in US) as such work seldom comes with the normal benefits that let you build a career in a non-exploitive way. I'd guess some of this will/does occur, but don't expect it to become standard.

Finally note that one of the key characteristics of a university is that it is a community. It is why universities want students (and faculty) back on campus as early as can be arranged. Partaking of that community is extremely difficult at a distance and impossible for a gig faculty worker. Thus, for students, the "college experience" is lost at a distance and the collaboration "serendipity" of the coffee lounge is lost for faculty. These are very important, even if somewhat intangible.
There is little joy or satisfaction in a completely transactional relationship.

I know a lot of folks as for advice here, but I've asked "Have there been..." to look for ways challenges have been addressed rather than asking "What are the potential challenges?" (as mentioned on in this comment). Is it possible to add something along those lines as well? Thanks!


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Any advice on developing a mini-course?
I was suggested to develop a mini-course that should last somewhere between a week and two weeks.
The subject of the mini-course is both advanced and niche -- material would be based mostly on my current work.
Target audience: roughly masters / Ph.D. students.
The course topic can be broadly defined as “Research in partnership with Indigenous Peoples”.
The problem is this: I have attended many courses and workshops myself and delivered more than a few PowerPoint presentations. However, I have never been part of teaching process, let alone developed a course. Now a potential opportunity presented itself and I do not know where to start (or whether to take the opportunity at all? -- it won't be particularly useful from career-building point of view. I am still on the fence).
I would appreciate any practical advice from active faculty on this subject.
What are most common pitfalls to avoid?

If you want a career inside academia, then teaching is going to be a large part of your daily activity. A course has to be the first course you teach, and this sounds like a good opportunity:

a mini course is not as daunting as a full course
master and PhD students know more, they know what to expect from a university course and can better deal with anything that you did not perfectly explain, and are often better at articulating what they don't understand. So they are a forgiving audience for a begining teacher.
You know the subject matter

The main pitfall for me when I teach a course on a topic that I am really familiar with is that I don't realize that something that is self-evident for me now isn't self-evident to the students. So I have to explicitly formulate to myself the level of knowledge and skill I can realisticly expect from the students and what I want them to be able to do when the course is over. Than I plan out the course so they can get from that initial state to the goal state. When doing so, I almost always have revise the goal state down: if you are really familiar with a topic it is really easy to underestimate how difficult it is to learn it. When I plan out my course and think about what the students have to learn to get from what they know now and what they should know at the end of the course, it becomes obvious that that is not possible given the time available in the course. I don't get frustrated by that, and I don't feel like "dumbing down" the course when addepting the goal down. It is more a process of me remembering that I did not learn this topic in a couple of hours either. Having a course with realistic goals, and most students reaching those goals is really rewarding. Having a course with too optimistic goals and most students not reaching those is really frustrating for me and the students.