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How can I start writing a research paper?
I'm a PhD student and I want to start writing my research paper on chemistry modeling. I don't know how to organize my ideas or how to highlight my results.
I'm looking for a strategy to follow, and even though I've been reading a lot of papers about my topic, I still don't get the starting point.

https://en.wikipedia.org/wiki/IMRAD have a look here, it might help. The IMRAD structure is widely used for scientific publications.

Related: https://academia.stackexchange.com/questions/122157/advice-on-writing-a-research-paper-in-a-less-time/122170#122170

A Ph.D. student often has an advisor to ask about such questions.

Start by writing a bullet point sentence for each paragraph summarizing in plain language what you want to say in it.

If certain things in your paper took you significant time to understand, and you were not able to find anywhere a clear explanation of those, add this explanation to your paper. If it's too long, add it to appendix. That's helpful for readers and also leads to more citations.

Read, a lot, and think about the structure of papers and arguments you are reading. Write, a lot, rewrite, think, rewrite. Understand the topic you want to write about deeply and thoroughly, but be open to revelation/new ideas/corrections while writing, thinking, or getting feedback. The importance of feedback from others on your writing cannot be overstated. Don't expect your first paper to be excellent. See it as a training and learning experience. Be patient as it takes a while to develope writing ability. And, yes, as mentioned, writing is a way to further develop your thoughts.

Congratulations on getting a publishable result!
When you're starting to write a paper, especially if you don't have a lot of experience with manuscript preparation, anything you can do to get past the blank page and start getting text down can help.
You've been reading a lot of related papers. Do you have any target journals picked out for this publication yet? Have you been reading papers from those journals? If you look at a few examples from your target journals, you can get a sense of the basic structure and organization they use. Put those section headings into your document. They will likely be Introduction, Methods, Results, and Discussion, but this can vary. Each section answers specific questions.
The first section to fill out is the Methods. What did you do? How could someone else replicate what you did?
Then fill out Results. What did you find out? What was significant, and what was not?
Now you are ready to write the introduction: What context would the reader need to understand why you picked this research question? Why was your research question important, what differentiates your strategy from other people's, and what was your contribution?
You can now write the Discussion, calling back to the context you established for your research question in the Introduction. Make specific references to your results and discuss what they mean in a more "big picture" way.
Finally, you are ready to write the abstract. This should summarize the whole paper, telling the reader in one or two sentences each why the research is important, what you did, what you found, and what it means. Basically, use one or two sentences to summarize each section of your paper in order.
That's it!
One last piece of advice: Don't be afraid to get feedback early and often, even if it is from your fellow PhD students rather than from your PI. The less developed your paper is when you solicit feedback, the easier it is to change course.

Beginning writers think of a paper as something that exists in their mind, and that the job of the writer is to 'download' it to paper via hands. This is not how it works. Writing is an iterative process, in which ideas are formed as you write them, and the writer moves from one draft to another, until it's good enough to send to the journal. So don't worry about perfection. Just keep doing drafts, and the paper will come to life, eventually.
Another thing that I think beginners miss is that the difficult part is usually just getting started, so I always advice my students to train themselves to start writing. This is achieved by putting a timer and promising yourself to work for say, 15 minutes. That time is usually short enough that you can avoid procrastination, but long enough to put something in writing. You then stop at 15 minutes, no matter if the writing is going well. You then force yourself to take a break and restart. Let's say you budgeted 2 hours of writing, that's 8 different times you have to force yourself to start. After a few days, your brain will be trained in the skill of starting to write.

I'm assuming that your paper will have the following sections, more or less in that order (the state of the art can be at the beginning or end of papers depending on fields, and sometimes fused with the intro):

Introduction what cool work you did in your paper and why it's important
State of the Art what other people did that are similar/related, what you are basing your paper on
Methodology the steps you took to achieve your results and why you chose them - sometimes also includes what you expected
Results a straight description the actual results and if they matched your hypotheses
Discussion now that you discussed the results, how do you interpret them more in depth? what do they tell you about your initial hypothesis? what follow-up questions did they raise?
Exploration (optional) if they raised questions and you did more experiments, quick summary (method + results + mini discussion)
Conclusion summary of the cool work you did + some perspectives.

If this is your first paper, it will probably be the easiest to start by the methodology and results description. Goal is to describe what you did, some of why, and your results, which you should know at this point. Then, I would suggest writing jointly the state of the art and the discussion, to make sure you are not overlooking things. Questions raised by your results might have answers in the literature, and doing a back and forth between discussion and existing papers will help you build a stronger argument.
You should finish by the introduction and conclusion: as they are summaries of your overall paper and how it fits in the rest of the science, as well as a way for you to sell your ideas, it will be easier (especially as a PhD student) to do them once you already actually have a paper.
Then you can do an overall re-reading to make everything simpler to read.
Good luck and have fun!

I really liked to work with this structure, where each section was one different latex file.
Much easier to work ... and to rework for the second paper (or the first paper, resubmitted somewhere else :D ).
I had the "rambling" section, which was equal to your "exploration". A lot of things put there, all related but all useless for the current paper...

Your starting point is reading tonnes of papers about your topic and in the type of journals you're targeting. You're already to good start.

A research paper conveys a key message to target audience and highlights the key contribution to the body of knowledge. It is not as broad as a Thesis.
Hence, in drafting a research paper, one needs to figure out and be clear in their mind ... what's the message I'm putting out there, what's significant about the work done, what's the purpose.
In your instance as you've narrated, you've got ideas already. Storyboard them and write them down.
Your results, itemise them and write them down. Also, write how you went about getting the results you've gotten. Slowly, the research paper is taking shape. With more ingredients, the paper is 'cooked', ready your 'dishing'.
There're different structures for research papers across different fields. For chemistry modelling, you should broadly fall under the IMRaD model.
I'll talk a bit more on this, before then take a look for instance at this GEOS-Chem chemistry model v10 by Keller and Evans (2019).
They have a structure introducing their work, the method used, deep dive into the work, followed by discussion and then conclusion.
1) Introduction;
2) Methods;
3) Long-term simulation using the random;
forest model;
4) Discussion;
5) Conclusions.
[Extract from IMRaD Wikipedia]
Introduction – Why was the study undertaken? What was the research question, the tested hypothesis or the purpose of the research?
Methods – When, where, and how was the study done? What materials were used or who was included in the study groups (patients, etc.)?
Results – What answer was found to the research question; what did the study find? Was the tested hypothesis true?
Discussion – What might the answer imply and why does it matter? How does it fit in with what other researchers have found? What are the perspectives for future research?

Please note that some have literature review (related works) as part of Introduction or better still just after introduction and before methods.
The literature review is rapid or purposeful. It's different from systematic review. However, some chemistry modelling papers are actually chemistry modelling reviews in which case they might be systematic review (aligning with PRISMA) or narrative review or even rapid following the PRISMA-ScR.
Also, take note that in some fields, methodology covers not just the methods, but the philosophical underpinning, research approach and strategy, methods and data collection tools. See the research onion in Saunders et al. (2023), now in the 9th edition.
Saunders, M., Lewis, P., & Thornhill, A. (2023). Research Methods for Business Students. (9th ed.) Pearson

Other answers give good advice on how to do this in general, I want to give some tips on how to do the practical thing. This is something I used to write all my papers.
In my opinion, separating the task of thinking from the task of doing is essential in overcoming mental blocks. If I'm trying to think about the overall story of the paper or proper language while I write down the content, I get stuck.
I employ a two-step process: First, I write everything down that I can think of. Anything related to the paper, what I did, why this is good, why it is better than other papers, what the application is etc. Crucial for this step is to not think about whether those claims made are correct or even make sense. After this, I usually have a draft of a paper that comes close to the required pages but the content is probably 50% nonsense, the language is bad, the pictures look bad...
So then you go to step two: Improving the content.
Now that there are some ideas on paper, it becomes much easier to get the actual paper that you want to write. Since judging content is simpler than creating content, I can now dissect everything I wrote. I find a lot of nonsense during this process, but some ideas stick and turn out to be good ones. It is also easier to judge the overall story from this, which helps to improve the structure. You do this a few times, filter out the bad stuff and keep the good stuff.
Two additional points: First, I like to get a bit tipsy to do the first part, but that is just me. Whatever helps you to produce a large amount of 'nonsense'. Second, an important skill is to not be afraid of reading your own text. This is something I struggled in the beginning of my PhD. Try to get over this, it is crucial for becoming good and fast.


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How should I interpret a suggestion to "synthesize" two sections of a paper?
I have submitted a manuscript to a journal. After some months, the submission is in the revised statute.
One of the referees suggested the following to me.

Sections 2 and 3 should be synthetized

What should I do over Sections 2 and 3?
My field is math.

Congratulations on submission... Google says it means to combine...

@PraphullaKoushik You are welcome.

In general, people say “thank you” when the other person says “congratulations”.. :) never mind...

@PraphullaKoushik Ok I got it! Thank you.

Synthesize in this context means to merge the sections into a coherent whole. So the reviewer is probably suggesting that these two sections would make more sense structurally (from their perspective) if they were combined.
Beyond this, it is not possible for us to understand the exact purpose of the reviewer's suggestion, as we do not have access to the article you wrote, nor the rest of the review(s). In general, suggestions or comments in any review are best understood in context -- what is this reviewer's understanding of the paper? What is their likely background? What did they think of the paper overall; which sections did they like and dislike? Based on the answers to these questions you may get a better idea of why they are suggesting merging the sections, and how you might go about doing it effectively (or alternatively, how to respond to the reviewer if you disagree).

Thanks for your complete and nice answer.

In addition to the meaning of this word in English, this may have been a mis-translation (a false friend from the referee's native language).
If the referee were Italian, for instance, they might have meant that you should reduce the length of these two sections.

Although, I have accepted the first answer, I really like to interpret the word ` synthetized' to reduce the length. Thanks for your useful link.

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How can I attract good postdocs?
I work as a research group leader at a top-100 university in Europe and supply of good PhD students is good, both from within the university and from other places in Europe. However, attracting good postdocs is much harder, even for the more senior professors with an even better international reputation than I have.
My impression is that the good postdocs are really picky with the places that they want to go to. It's the Ivy league places in the States, Cambridge, Oxford, ETH or EPFL. They don't seem to even consider any other options. I have tried to talk to good finishing PhD students in groups that I know, but they don't seem to see my university (or my group at least) as a good career choice.
How can I change this and attract good postdocs?

There is a lot of heterogeneity in Europe regarding postdoctoral working conditions. I don't know if this is the case where you are, but in some countries, like Portugal, postdocs don't have all the rights of standard employment. For me, this is a deal breaker, independent of institutional prestige and quality of research.

Pay well, provide stability?

I'm curious to know which field of research you are in. In my field of research there's always an over supply of good postdocs and an under supply of postdoc positions.

@AnderBiguri Neither of those things are probably in the gift of the OP, but more likely decided at a university level.

@IanSudbery well, one hopes that permanent academics can try to exert the little influence (or at least, voice) they have in the university. Plus its not entirely true, in the UK as a postdoc your salary can range for more than 20K£ of difference. I can tell you that hiring for the higher pay and longer projects will attract people. You can write grants with that in mind, for example.

@AnderBiguri Universities are not run by academics. There are probably location and disciplinary differences. But e.g. all PDs are grade 7 at my Uni, which is £37k-£45k. And HR want a very good reason if you want recruit someone beyond 7.1 (£37k) even if you can convince UKRI to fund higher (I've seen requests for 7.5 rejected by funders, although I have successfully gotten 7.8 funded once before). As for length - most grant calls have a soft 3 year limit. There are a small number of schemes allowing 5 years, but acceptance rates are 5% rather than the usual 20% for 3 year calls.

@IanSudbery this is my 7th year as a RA in the UK, I am well aware of how the system works. I insist that if you as an academic have no power, then there is no power and the answer is "screw all of this, let universities fall down", which I think is the least desirable solution. You have little voice, but you do have the most voice of all people involved.

Which subject you are talking about?

@AnderBiguri Increasing many of us are in the "burn it all down" camp. Those of us that arn't see the solution in national level reform, probably brought about by a prolonged fight against the basis of the system. But that doesn't help individual labs or postdocs in the immediate future.

Year on year, I have a good proportion of students in my cohort that clearly can't understand even basic English, and the only words they know how to say in class are "attendance code" (sometimes they also add "please", but that's rare). Every year we get students with the completely wrong background, our cohorts keep struggling with maths, and we keep getting told to just "remove the maths from the lectures" (aka lower our standards). And this is completely out of my control, as an academic. We try using our Voice on the admissions office, but alas, they don't listen. We have no power.

I don't think that there is an easy solution to your problem. If there were, and it were easy to put into practice, all the other less-famous labs would also put it into practice and the easy solution would no longer work. It's an old problem in economics.
That said, however, I think two parts of a solution (and by no means all of the solution) are the following (I ignore things like grant money, the fact that you are in Europe, etc. because you either can't change them or will already be well aware of them) :

Be a good person to work with. Treat your colleagues well, treat your students and post-docs well, share your ideas.
Increase your sales taskforce. You've probably never thought about the problem that way, but if you are the sole sales-person for your lab, then you are behind the eight-ball. You will find it very difficult to compete with the publicity that other, better known places, command. There is nothing shameful about asking people whom you know and who like you to advertise your good points (that's what post-docs do when they as you for a referral!). So, if there are postdoc who have worked with you or who are currently working with you, and with whom you enjoy a good collegiate relationship, mention to them that you are looking to the future. Tell them you'd be very grateful if they would mention your lab to any third person (potential post-doc?) whom they think worth telling.

To see how important, ultimately, it is to work with people who are friendly, supportive, challenging, collegiate, and all-round "nice", you need only look at the number of questions on this forum (see this example, and this) that are phrased along the lines of "HELP! I'm working in a famous lab with lots of money and a famous PI ... but the PI hates me and I hate them"!

slightly related to "sales force": What are some innovative techniques that new professors use to populate their new laboratories with students and postdocs? (besides advertising)

This is tough.  The job market for assistant professorships is so tight that talented postdocs will try for the highest profile jobs that they can find in order to be competitive when they enter that job market.
So, if you want the best postdocs, you'll need to convince them that your environment and publication record is high profile enough to attract them.   When you can say "I've hired 10 postdocs, and 9 of 10 of them moved on to stellar academic careers", you'll no longer have a problem.
That said, when you hire a postdoc, you're intrinsically saying that you'll be hiring a person with academic job aspirations.  Every postdoc you hire will be looking toward that next job.
Presuming that you're looking for people to do the work your lab needs done, and not necessarily looking to train the next generation of faculty. an alternative approach would be to hire people that you need to do your work as normal employees, not aspirants to academe.  Look for staff scientists and the like.

I'll add that the postdoc market is a networking thing, not necessarily a "I'll post the add and the applicants will pour in" thing.

"9 of 10 of them moved on to stellar academic careers"  That's not going to happen.

Offer a position with a salary, rather than a stipend.
The position should also offer (paid!) teaching opportunities, for those who want to improve their CVs.

Why is a salary better? It may have tax implications.

@Buffy this will vary regionally, but in Europe, having a stipend instead of a salary forcibly removes you from all social benefits (health care, social security, pension contributions) and all the standard employee rights (legal protections for hiring/firing, collective salary agreements, holidays, sick & care leave, mediation). For some people, the smaller employee perks (subsidised childcare, mental health care, cheaper meals) might also add up in a big way. This might not matter in some countries, but in those set up around social benefits, it's a bad sign.

I'm guessing that outside of Europe, this distinction probably doesn't matter as much because the system is set up very differently.

@Buffy Yes, salary is taxed, which means it counts toward pension. Also, In Sweden you get 80% of your salary during parental leave. A stipend counts as 0, so this makes a big difference. Post-doc time is  a common time when one starts a family, so this distinction is rather important.

Stipends have been taxed in the US since the Reagan years

Stipends for postdocs are not common in Europe, getting a salary and a work contract is much much more common.

@Dr.Snoopy My Swedish department has a yearly stipend for hiring postdocs. But it is indeed unusual; it is awarded via a foundation (big donation to the department by a private donor).

@coffee_into_plots In the US this distinction is not as stark as it apparently is in Europe, but it is still there.  For example, stipend recipients do not receive unemployment insurance, do not have taxes withheld from their checks (their checks are not "pay", they are "stipends"), have to jump through hoops to get loans because they don't actually work for anyone (i.e., legally they're not employed and hence have no employer), etc.  I did it for 3 years and it wasn't horrible, but it was a bit of a pain.  That said, not all postdocs are viewed as stipend recipients...some are employees.

@PerAlexandersson Correct, stipends are taxed but only employers can withhold tax.
Since stipend recipients are not employed they are also not payed, making them responsible for withholding their tax and making their payment to the IRS.  This is one of the many pains of being a stipend recipient as opposed to being an employee.

@Buffy In the US stipends are also taxed.  The main difference of being a stipend recipient is you lose a lot of (maybe all) of the legal protections of an employee/employer relationship.  Please see my previous comments for such examples.

@tnknepp, the question seems to be about the situation in Europe, not the US.

If the position comes for a salary of 100% of regular employment time, the teaching does not have to be paid extra. In fact, it would be quite strange and might require extra time spent on the teaching.

In what European country does having a stipend instead of a salary forcibly remove you from health care? This sounds highly unusual to me.

@RichardHardy (For Sweden) It does not remove you from health care. But unemployment benefits and maternity leave support, is based on your last few years salary. Since scholarship is no salary, this means your benefits will be on the minimum level, not 80% of a normal salary.

Right. I have more examples like this, so I was wondering if there is even a single country in Europe where having a stipend instead of a salary forcibly removes you from health care. I forgot to address my comment to the right person, though; it is @coffee_into_plots

@RichardHardy here's a link that explains the situation e.g. in Germany for PhD students on stipends. https://thesius.de/blog/articles/krankenversicherung-promotion-stipendium/ Basically, you'll need to find a workaround since health insurance is mandatory, which is expensive- you pay your own employer contributions, or private insurance. This is forcing you out of the job -> health insurance part of the system.

@RichardHardy Having paid into the system and showing that the country is your centre of life (so that you likely pay into the system again), e.g. by being a paid employee for a minimum amount of time, is a requirement for being eligible for socialized health care in Austria.

Sounds great, but nothing we have a choice of. Postdocs are salaried in the UK, PhD students are on stipends. No choice in the matter. Also, whether you can offer any (paid or unpaid) teaching opportunities to your postoc is often out of your hands. I was begging (even for unpaid) teaching opportunities, and in the end we couldn't get the approvals so my (then) supervisor just let me try out while sitting in on the lecture. Now (same department), the situation (read, the head of school) has changed, so now we can usually offer those kinds of opportunities to interested postdocs.

To get good postdocs, I think you first have to get a lot of applicants.
To get a lot of applicants, offer a lot of money and a lot of freedom. Offer a lot of career support for obtaining a permanent position.
If you have to offer less of one of these you may need to offer more of another.
And, those top schools you name generally offer a lot of the last item, which is likely the reason you ask this question.
Of course, this might not be possible or desirable in your context.
FWIW, I've seen the above suggestions work in practice.

It's hard to be competitive on pay.  NASA's postdoctoral program currently has a base stipend of $70K/year (plus locality adjustment, insurance), plus $12K in relocation expenses, plus a $10K/year travel allowance.  I've seen DOE postdocs making over $110K/year.  That's tough to beat.  Do you have a gauge for what postdocs in academia make?

@tnknepp, no, sorry. And it varies a lot by place and by field.

@tnknepp... postdocs in academia? not enough. At least in the US, postdocs in academia make so little that they qualify for government housing here in the US....

I think you are seeing the effects of the pyramid structure of academics. There are more PhD students than postdocs and more more postdocs than professors in academics overall. This means that not everyone who does a PhD at a top university will get a postdoc there and not everyone who does a postdoc will get a professorship there.
This means that at a university like yours that is good but not the very top, you will still have a good proportion of professors who did PhDs and postdocs at the very top  universities before coming to your university. In other words, if you do try to rank people by their academic achievement you should expect that the average level of your professors is higher than the average level of your postdocs. Of course, trying to linearly sort everyone by their academic achievement is a gross oversimplification and as the other answers explain, networking, being a welcoming research group and offering attractive positions will help attract good postdocs.

A few things come to mind in addition to several of the important points raised

The Postdoc should provide an attractive compensation for those high aspirations that the University and project has (and they should have to a reasonable extent).

The Postdoc should be able to reasonably support the candidate's livelihood and personal needs. For instance to bring his family and return his family. Its not worth it if a Postdoc saves 6 months to bring his family under a one year contract and needs to save another six months to return them back.

Postdoc should reasonably give the candidate some room to express and explore his Academic philosophies e.g. the kind of top journals he might like to publish, the kinds of networks he would like to build.

The Postdoc should socially make the candidate look like someone working on a decent job in a foreign land. This has to do with pay and the job conditions should cushion some national policies and benefits that puts locals at a higher social pedestal

The institution, supervisor and lab should look attractive, adding value.

The postdoc experience should be able to add value in the sense that the candidate can even negotiate for greater opportunities in that country and the rest of the world afterwards.

The postdoc opportunity should give some reasonable time before expecting those high quality results and papers. Strong research footprint requires some time.

@Trunk, I get your point. There is a huge spectrum of what different countries and institutions offer, as well as the cost of living and benefits in those places, especially for foreigners. For #5, keeping other things relatively constant, this point is a reality that many live by.  Prestige has its place, and many of those top institutions have higher expectations and ways of managing things, as that is what fuels their reputation. Similarly, a top professor in an area usually has a higher "taste of quality".

This is partly a marketing problem, as in marketing a service or goods. You can describe this is in several different ways, one is like this:

What is your intended target group, ie what people do you think should know about and have a positive impression of your program?
How do you reach the intended target group? Do they even know that you exist? What marketing do you do towards your intended target group?
How does the intended target group perceive your offering? Do they find it attractive or are there things missing in the initial offering?
What does current postdocs think and say about beeing part of the program? Is anything really good: make it public, is anything really bad: change it!
What does your alumni think about the program? Do you keep contact with them and use them in your marketing?
What does your grant donors / other cooperation partners think about your program? Do you use them and their contacts to reach out for new postdocs?

Another part of the problem is "sales". Sales is very much about filling the pipe-line of "customers" and handling them well. So how do your organization identify potential customers (suspects), contact them and make them interested (prospects) and get them to actually apply for postdocs. Reaching out to suspects could be done through various methods, one guess would be to scan published papers in the relevant area and contact the authors telling about your offering. What happens if someone contacts you -- how do you respond and is it timely?

Pay your postdoc a livable salary. None wants a miserable life.

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Can a referee request a paper referenced in the reviewed paper?
If you review a paper which relies on results some other paper and you do not have access to that paper, is it acceptable to contact the editor and ask whether the author can provide a copy of the referenced paper? Are requests like this reasonably common?
Or should the referee simply take the word of authors that their conclusions based on the referenced paper are correct, even without seeing that paper?

Yes, if the paper is crucial to the work, I don't think there is anything wrong with asking the editor to provide it to you. I think the editor would probably check for it himself first (in order to save time), and if not possible would relay your query to the authors. As an extreme measure, if the editor was unwilling to do this, I would simply consider writing back saying you are unable to fully review the paper because access to this crucial reference was not provided.
So, in short: do not let your lack of subscriptions get in the way of doing of thorough review.

Now, there are some other ways around this. First, maybe you can find that paper in the usual ways: through interlibrary loan or on the “grey market” (ask a friend who's got more comprehensive subscriptions that yours). Second, maybe the editor offers reviewers some service that can be of help already (for example, Elsevier journals offer a 30-day free access to the Scopus database to their reviewers).

There are two aspects of the question: Should you try to find the necessary information (papers) to do a good review? And should you contact the author of the paper you review to ask for other sources written by that author?
It is clear that you should attempt to gather all information you deem necessary to perform your task as reviewer. Since journals typically only accept published materials to be used for sources (with the possible exception of unpublished data or personal communications) you should be able to find such information given some time and work. That said, I doubt that many would keep a review on hold just because they have not been able to find a specific source unless that source is absolute key for a critical (in the negative sense) aspect of the paper. It is, however, possible to inform the editor that you have not been able to check up on this particular aspect since you are unable to obtain a copy of the paper within a reasonable time. Although it is always possible to purchase papers from publishers, I do not think we consider such actions within the expectations placed on a reviewer.
Now, the second aspect about contacting the author for more information should be handled with care. As an editor, I would first of all want to be aware of such communications. Peer review is based on an objective evaluation for materials and although a simple request is not likely to change much it simply removes part of the desired distance between author and reviewer. One solution to this, which I would prefer is for the reviewer to contact the editor and ask for the material (from the editor or from the author through the editor). It has not happened to me that i have received such a request but I would not consider it other than a positive. I would also add that if a reviewer is lacking some key piece of information (as stated in the previous paragraph) I would greatly appreciate knowing about this weakness in the review. Given such information, I could, as and editor, add key comments of requests to the author to improve the paper in some respect.
As a side-point, I would like to add that some papers that totally rely on other previously published on, for example methods and error discussions, should include enough of a summary to make the paper stand on its own in its entirety. It is thus possible to request a major revision with the explicit wish to see additions to the paper to remove the necessity to have to read other papers for key aspects. I fully realize the delicate balance in such requests since no-one is striving for excessively long publications.

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How much time is usually left for authors to return page proofs? What happens if I am late?
Recently I was handling submission of a paper to a journal. I was somewhat surprised that I was asked to return the corrections to galley proofs in 48 hours.

To ensure fast publication of your paper please return your corrections within 48 hours. ...  Note that  may proceed with the publication of your article if no response is received.

How usual is it, that only a short period is left for the authors to return page proofs? Do many journals allow similar time span? Or is a longer period customary?
I can imagine situations in which I would not be able to respond in 48 hours.
What would happen if I reacted only later, not within the time period required by publisher (48 hours in this case)? Is it probable that they would still incorporate the corrections if I emailed a bit later? (Or if I emailed them that I am unable to complete this in 48 hours and explained the reasons.)

Since the link was edited away from the question, I just mention in comment that this Google search suggests that there is quite a lot of journals which require galley proofs to be returned in 48 hours period.

@CharlesMorisset but you do not seem to get any relevant hits with a search for 24 hours. This suggests 48 hours might be the lower limit.

With Wiley, the journal I edit has a one-week period for returning proofs. This is set by Wiley and not by the journal. If proofs are not sent in, at some point within another week, the typesetter will typically ask for the proofs through a production editor. This is because the typesetter has the manuscript along with, I would guess, hundreds of other proofs lined up in a production line and at some point they do not want things lying around for very long. So in this case, not much happens if proofs are late and I have never seen any serious repercussions from the publisher's side affecting authors. In the worst case a paper that has been assigned to a specific issue may be moved to a later issue since the production of issues (physical printing) is not possible to adjust other than under exceptional conditions. In the end, it will the author's loss if the paper is not published as early as it could. Since for most papers, electronic publication occurs before printing, the delay just means the paper appears online later by the same amount of time or more; it can be bumped in the production line of the typesetter in favour of those that come in on time.
In my experience, it is not possible to get corrections done after returning the proof corrections. One can always try but if the paper has been corrected and published online, there is no other option than to live with the problem or if it is in some way critical, go through the journal editors to possibly publish an errata.

For journal articles 48 hours is not uncommon. I have never experienced less and I have never had considerably longer. If you let most journals know when you can return them, they will generally either allow you to submit them later, but this will often result in the article publication date being pushed back. In some cases the journal cannot comply (e.g., special issues) and then they may attempt to publish without you reviewing the page proofs.
The idea of page proofs is that you are checking to see if any copy edits they made are correct and that the proofs are an accurate representation of what you sent in. It shouldn't take very long to review the proofs (a couple of hours at most).

The publisher Optica has reduced their deadline to 24 hours.

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


text:
What are the essential points that should be covered in a dissertation abstract?
I need to prepare a 2-page abstract of my dissertation as part of a funding application. What are the essential points that such an abstract should cover?
This opportunity (and my PhD) is in the social sciences, and I know the points regarding tailoring the abstract to the opportunity advertised. But still what is the sort of information that the recruiter would scan my abstract for? For instance, I have seen Profs run their finger down a 2 page list of publications in an application; only occasionally pausing at some journal names. What are the fingers of my evaluators going to pause at?

Any abstract should cover 4 elements: context, problem, solution, and validation, in this order. The main thing you want to highlight is the contributions of your dissertation. The context and problem descriptions are essential to try to make your contributions understandable, and to convince the reader that what you have done is important. Describing the validation is important so that you convince the reader that what you have done is correct/valid.


text:
Who is responsible for detecting plagiarism in a PhD thesis?
Background
I am asking this question in the context of the long running plagiarism scandal in Germany.The most prominent victim of the scandal of plagiarized doctoral dissertations by politicians was former defense minister Guttenberg. His doctoral title was withdrawn, and he resigned from his position. He was followed by several other politicians, and now even the German Education and Research Minister Annette Schavan is under suspicion of plagiarism.
The interesting thing is that for all these people, the plagiarism was detected only due to plagiarism detection wikis like VroniPlag and GuttenPlag, where ordinary people compared these doctoral dissertations with other published work. The only role of universities has been to respond to allegations that are especially well documented and have caused a reasonable amount of public uproar.
Don't the Universities themselves bear any responsibility for letting this plagiarism go undetected? In fact Guttenberg's dissertation was awarded a summa cum laude. It appears as if their is no mechanism whatsoever (at least in German universities) to detect academic fraud.
Is there any mechanism at all to detect plagiarism or fraudulent research in PhD dissertations (doctoral theses)?
I understand that there are probably country based differences and my experience is primarily with the German system. Still it would be good to know the seriousness with which academic fraud is taken in different countries. This appears especially pertinent to the maintenance of the credibility of academia in general and doctoral degrees in particular, and yet there seem to be no checks whatsoever!

Short answer to the title question: The author!

There are a variety of tools available for checking student essays for plagiarism. Is there any reason, other than perhaps needing more journals added to their databases, that they couldn't also be used to check for large scale abuse in theses?

Where not all of these cases with PhD thesis's in arts and humanities (Geisteswissenschaften)? I think in natural sciences / engineering this form of copy & paste plagiarism is not really possible like this.

@MartinScharrer: Most of these cases wouldn’t even be PhDs (but LDs or similar) in the anglophone system, if I am not mistaken.

I'm coming to this late, but I'd love to know why the word "victim" is used in this context.  Someone caught having plagiarized their dissertation is a victim?

The problem is that the PhD system is designed for people who intend to become researchers.  For these cases, plagiarism is not at all a common problem.  You are expected to published your research, and you will not have a successful career unless it is widely read and cited.  That gives lots of opportunities to get caught, and the penalties for plagiarism are a huge deterrent.
To the extent you find plagiarism, it's generally people who do not want a research career, but instead view the PhD simply as an obstacle on the road to a teaching (or other) career.  Probably the community should scrutinize these sorts of theses more carefully, but it can be hard to work up the energy to do so when most of them are OK, and when these theses really don't matter much for the research world.
The German politicians are pretty much the worst case scenario.  In the US, the stereotypical case is educational administrators.  Typically, you have a distinguished person who starts to feel the need for a PhD.  Perhaps it's because they associate with academics and feel looked down upon, or perhaps it's because an academic endorsement would make the public value their expertise more.  This student is very smart and accomplished, and nobody suspects them of any dishonesty.  However, they are also very busy, often working on a PhD while pursuing other projects as well, and academic research is not a priority.  At some point, they succumb to pressure and start taking shortcuts.  Probably it starts with small things, but the shortcuts gradually grow larger.  They rationalize that the thesis doesn't really matter anyway, because they have no intention of following an academic career track.  After all, they have the knowledge and experience, and they deserve the PhD title, so what difference does one document make anyway?  Meanwhile, the advisor probably doesn't spend that much time working with the student, and has no reason to suspect anything.  The advisor really ought to be extra careful in cases like this, but that would seem like an insult to the student, so it's easiest just to trust them.
So my take on this is that plagiarism is not as widespread as news stories might suggest.  It's just particularly likely to happen in cases where it would attract media attention.

Given the complexity of the modern PhD thesis, and the number of references to other works in the literature that such a work would normally contain, being able to catch plagiarism can be difficult. This is especially true when you only have a printed version of the thesis to work from. Moreover, the time to review a thesis is normally quite short—a few weeks to a month at most. Given the number of other responsibilities most faculty members have, it's unlikely that they're actually able to verify every fact and every citation, let alone check for evidence of plagiarism!
On a general level, it is also assumed that everybody plays by the rules, and that therefore plagiarism shouldn't be likely in a PhD thesis. Only if suspicions somehow get raised do people take a second look. It's probably an invalid assumption, but it keeps the system moving. Unless we want to move to a QA-like scheme in which every claim and source has to be verified against the original, I'm not sure what other options there are.

Plagarism in journal publications is a large concern because the professors are often running their own labs, doing their own research, with very little oversight. The only chance to catch fraud is through a careful analysis of their publications, which is done both by the publications themselves, their peers, and the public at large.
Regarding PhD theses, the student is working with an advisor, doing (hopefully) original research. Any actual publications the student submits will go through the peer-review process, which will hopefully find any plagiarized references. Regarding the dissertation itself, it's often simply cut-and-paste from their actual publications, and once submitted, never read again.
It's likely for this reason that people probably don't dedicate much effort to finding plagiarized works in their thesis. The student is doing original work, as verified by their advisor and their committee, and any publications by the student have been peer-reviewed. No one cares about their thesis, and if they try to continue their behavior as they progress in their career then they'll simply get caught when it actually matters (i.e., during the peer-review process) in the future.

The part about original work may be true in the experimental sciences, because you can see what the student is doing in the lab (well, they might be committing fraud with the results, but you can tell they are doing something).  By contrast, in math if someone comes to you with a proof, you can't tell where they got it.  If it's great work, then you'll probably recognize if it is plagiarized, but if someone digs up an obscure paper and recycles part of it, there's no way of knowing without a search.  This may be a poor thesis, but a poor thesis can be enough to graduate.

By contrast, in math if someone comes to you with a proof, you can't tell where they got it. — Really?  I find (at least with undergraduates) that a few detailed questions about their thought process ("That's cool!  How did you think of that?") usually uncovers whether someone really worked out a proof themselves.

@JeffE: Yeah, if someone tries to pretend they came up with something clever, they will likely get caught.  But there are a lot of junk papers that are boring, poorly motivated in the first place, and involve only pretty trivial proofs, but are correct and have some (minor) originality.  This won't get you an academic job, but it could be enough to graduate with a minimal thesis.  If you really interrogated the student, you could probably catch them.  However, if you have a struggling student who comes to you with such a paper, you'll probably just feel relief that they can actually graduate.

This is not a proper answer to the question at hand but since Ivar Persson used the term "responsible" - I only see one responsibility*: The responsibility of the PhD candidate to follow the main academic goal: the search for the truth with true methods and true intent.
Do we really blame mentors (or: advisors) for failing to detect plagiarism when the problem is on the other side of this mentor-mentee relationship? .
* for a responsibility term close to what Christopher Avery proposes

It seems like no one thought of who sounds obvious to me: the PhD examination jury. It bears the responsibility to award the thesis, is made of international experts of the field, and should therefore be able to detect ideas that have been borrowed; also the advisor, who supervised the work, has a prominent responsibility among them.
I do not buy the argument according to which an advisor might have trouble detecting plagiarism of a obscure paper: she often propose the questions to the student, and should therefore know the surrounding literature.
More precisely, there may be cases where the plagiarism is difficult to catch; nevertheless, right after the author these people, to who the university asks whether the work deserves a PhD, have the main responsibility.

Not all countries have a "jury" system like you describe.  For instance, in the US, a PhD student typically has a "committee" of professors from her own university, and it's quite common that the advisor is the only one who's an expert in the student's specific subspecialty.

The advisor "should therefore know the surrounding literature": In general, yes, but IMHO it's unreasonable to expect the advisor to be familiar with every relevant paper ever written.  If you look at all the papers cited in your students' theses, can you honestly say that you knew about every one of them before the student did?

This is putting the cart before the horses. The advisor and committee have the job to find out whether the work is of quality and sufficiently original to warrant a PhD. However, bar a glaring blunder in the checking progress, the team should be able to assume that the candidate did not act in blatant contravention of academic standards. If you demand a complete checkup, you establish an atmosphere of distrust. That may be appropriate in banks where large amounts of money are handled or in the secret service, but it doesn't belong in science. I wouldn't want to work in such an atmosphere.

@CaptainEmacs: I fail to see how the advisor and committee could be considered responsible for finding out "whether the work is (...) sufficiently original" and not to detect plagiarism, which is the least possible level of originality. I am not saying that they should always check for plagiarism, but that they have a strong responsibility to detect it. By their knowledge of the field, the oral defense (in countries where it exists), the regular talks with the candidate (for the advisor) they should be able to detect plagiarism in many cases.

@BenoîtKloeckner Yes, of course, that's what I mean by "bar a glaring blunder". I doubt, however, that they are responsible in a case of outright fraud, i.e. a competent attempt to hide the plagiarism; which is what I would expect from a "competent", i.e. plagiarism-aware, but malicious PhD candidate. If we have a case of an "incompetent" candidate who commits "unsophisticated" plagiarism, the question is how they could have been considered as a suitable PhD candidate in the first place.

All of the candidate, his/her advisors, examiners, colleagues and peers have levels of responsibility for detecting plagiarism, however it is not the primary objective of a Ph.D. system. The primary objective is to determine whether the candidate has the ability to carry out research, think logically and clearly about that research and communicate the results of the research, the implications and possible directions for further research based on the results.
When it is detected, the serious consequences (loss of reputation, loss of career, public exposure etc.) are the principal deterrent to others. Of course advisors and examiners should be actively on the lookout for plagiarism however their principle activity is to advise on the development of the work and examine the result of the work. Ph.D.s are, in some cases, supervised and examined by early career researchers, who may not have the depth and breadth of knowledge of the literature to detect some cases of plagiarism. No matter what, the candidate carries the ultimate responsibility.
No system we can devise will ever be perfect.  Students are not often given much guidance about what constitutes plagiarism, other than having to sign and agree to be bound by the universities policy on it. There is far more advice available now than when I did my PH.D., and many more sources of advice on what constitutes plagiarism.


text:
Citing an article under a double-blind review process
This is my case: I've recently co-authored and sent an article to a journal that follows a double-blind review process, so that reviewers shouldn't be able to know the name of the authors. ---I mean, I (as the corresponding author) am responsible for hiding any authoring information to them.
Now I am writing another paper and I want to cite the article that is under double-blind review.
So, it is not only that I should add the typical "under review" label when citing that article, but moreover I can't give any information about the article that may spoil the double-blind process. For instance, if I add the name of the authors and the name of the journal it was sent to, then I can't include the title of the article (because it could happen that the citing article is sent for reviewing to one of the blind reviewers of the first article, or that it is even published before the first one...).
Anyway... How can/should I cite an article that is under review by a journal that follows a double-blind review process without potentially revealing too much information?? How is this problem usually solved?
I must say that I usually publish pre-prints as technical reports, but I didn't do it this time, in order not to reveal any information that could be accessed by the blind reviewers.
EDIT:
I was thinking about putting this label instead of the title of the cited article: "[Title is omitted to protect the double-blind review process]". But I still have some doubts. If I mention the name of the journal it was sent to, could the article be potentially recognized by the blind reviewers?

Which field is this? The journals in which I publish never allow references to articles that are not at least accepted for publication.

@Cape Code, the article I am just writing now deals with Quality Control and Operations Research. The author instructions of the journal I am planning to send the article to say the following: "Unpublished results and personal communications are not recommended in the reference list, but may be mentioned in the text. If these references are included in the reference list they should follow the standard reference style of the journal and should include a substitution of the publication date with either 'Unpublished results' or
'Personal communication'". (cont.)

(cont.) In my case, it makes more sense adding the unpublished article (the one under a blind review process) in the reference list, as I am going to cite it several times.

@Cape code: Interesting. In my field (mathematics) people cite preprints all the time and nobody bats an eye.

@Nate Eldredge. That is the point ---it is usual practice. The problem here is that the pre-print I want to cite is sort of protected by the double-blind review policy of the journal.

@NateEldredge in fact the criterion is 'publicly available' so preprints are fine, but not manuscripts in an ongoing peer-review process.

@Cape Code: I am talking about preprints of papers currently under review, or even preprints that have never been submitted at all. Of course, you want to be proportionally more careful about relying on unpublished results.

@NateEldredge yeah, I get it. The publishing process in my field is shorter than in Maths (it is in the order of 1 to 3 months) so preprints are rarely (if ever) made publicly available prior to official publication. During peer-review, articles are only available to editors and reviewers. If the article is ultimately rejected, the citation is obsolete and journals don't like that.

It might be worth asking the journal editor.  They could have some policy for what to do, or they could just ensure that they won't assign it to the same reviewers.

Considering the following extreme case can help to clarify: what will you do if article B is accepted before article A finishes peer review?  This could easily happen, given the high variability in time in review cycle and number of reviews.
At that point you've got basically two options:

Drop the references.  Can your paper survive without them?  If so, it's not a big deal.
Put your blind review article into a pre-print archive, in order for it to be available.  This might "spoil" the blind review process, but only if the reviewers go looking for it and only if it significantly changes their opinion.

In the mean time, I would recommend citing it as "[omitted due to ongoing blind review; available on request]", and letting the reviewers request through the editor if they feel reading your pre-print article is important.

But would you add some information about the authors and/or the journal?

If I'm blinding, I generally blind the whole set of information.  You certainly can't say the journal, since the journal might decide it doesn't want your paper.

You can cite is as "Author names omitted due to the blind review", "Your paper A title", under submission technical report available upon request.


text:
What is the best English equivalent for the Spanish 'Profesor Contratado Doctor'?
This is a question about academic ranks or positions. I am interested in knowing the best equivalence for the Spanish 'Profesor Contratado Doctor' in English language (UK, US, etc.).
Description of 'Profesor Contratado Doctor':

tenured (i.e. permanent) position,
not a civil servant,
not an entry-level position to the tenured track,
is the previous position to 'Profesor Titular de Universidad' (which is sort of equivalent to the Associate Professor position).

So it is something between Assistant Professor (or Lecturer) and Associate Professor. Is it a sort of 'Non-civil-servant Associate Professor', 'Senior Assistant Professor', 'Assistant Professor with PhD'...?
According to Wikipedia (https://en.wikipedia.org/wiki/Academic_ranks_in_Spain), 'Profesor Contratado Doctor' can be expressed as Associate Professor (but not a civil servant yet). I am writing the current question becauase I want to be sure about whether Associate Professor would be the best way to translate this Spanish position or not. I would like not to mislead anyone when I say I am an Associate Professor (meaning 'Profesor Contratado Doctor'). At least, I would like to mislead as little as possible.

EDIT:
I've seen in Wikipedia and also in this other thread here that mapping academic titles or positions from one country to another is really very difficult and there are too many particular cases.
So, maybe the point is finding a neutral, generic classification, something that can be understood for everyone. Therefore, assuming that we have the following kind of generic tenured positions (sorted in ascending order):

Assistant professor (entry)
Associate professor
Full professor (top)

what would be a name for something between 1 and 2?

EDIT:
More facts:

In this WordReference thread they conclude that Associate Professor is the most appropriate translation.

This sort of official PowerPoint presentation states that 'Profesor Contratado Doctor' is equivalent to 'Assistant Professor (tenure track)'.

This report says that a 'Profesor Contratado Doctor' is a Lecturer.

Irrespective of what the best translation of this title should be, there is a  problem with the way you are using the term "civil servant."  I suspect you are using this as a calque of a term from another language like Spanish.  In English (American English, at least), "civil servant" just means "government employee," although it is most typically used to describe people in permanent, mid-level positions.

@Buzz I do mean civil servant. In Spain, Full Professors and actual Associate Professors ('Profesor Titular de Universidad') are paid by the Government (and they have all the rights and dutties associated to being a civil servant). Unlikewise, 'Profesor Contratado Doctor' is a tenured position but it is paid by the University.

@Vicent, at public universities in the US, ALL the employees are paid by the university which IS an arm of the government. So everyone is a civil servant and paid by the uni. This may be a distinction of some importance in Spain, but it's not in the US. At private schools in the US, NONE of the employees are paid by the government, but all of them are still paid by the uni. That could make the title hard to translate exactly.

@BillBarth  Here in Spain, (public) universities also get their fundings mainly from the government. However, there is a huge difference between being paid by the university or from the government itself (it is a different status).

@CapeCode Thank you for editing the subject of the question.

Note that "lecturer" means different things in the US and UK. The UK meaning may be close to what you described; the US meaning is not.

It is often difficult to map (academic) ranks between countries and languages. There might be subtle (and sometimes not so subtle) differences, that make a perfect mapping impossible.
I would write something like: "Associate Professor (Profesor Contratado Doctor)". In that way you provide your official title (no confusion), and a title the reader can relate to (clarity).

This is what I am actually doing, now that I've become a Profesor Contratado Doctor. Therefore, I mark it as an 'accepted' answer.

I occupy one of these positions, so I can explain it.
In the Spanish system there is no concept of tenure as such. There are two kinds of permanent profesorial positions, catedratico and profesor titular. Employment as either means that one is employed as a funcionario de carrera, which means a civil servant with all the accompanying civil service protections. In practice this is quite similar to tenure, but the manner of obtaining such a position is different, and as I remarked there is no accompanying notion of tenure. The relevant civil servant status is essentially the same as that of a postal worker.
A profesor contratado doctor is also a permanent position, and also a funcionario in the sense of being a public employee (but not a funcionario de carrera), but is technically different in that it is a laboral position, which in practice means that such a position is in principle susceptible to forming part of a layoff package (although I believe this has never been done with respect to these positions) and that the employment conditions are subject to collective bargaining as they would be for truck drivers.
Spanish administrative law treats the two kinds of position rather differently, and while in practice a profesor contratado doctor earns only slightly less than a profesor titular and has generally essentially similar working conditions, also in practice there is a hierarchical relationship and profesor titular is treated as above profesor contratado doctor.
None of these positions is susceptible to promotion in the usual sense. Obtaining any one of these positions requires competition against all qualified applicants.
In practice Spanish universities have used profesor contratado doctor positions more in recent years than in the past because austerity measures made offering civil servant positions more difficult and the laboral positions were easier to offer. The typical occupant of such a position has had several postdoctoral positions and is considerably more active in research than profesores titulares of the previous generation.
Such a position has no real comparable in the US system, but simply Professor probably comes closest in practice. Associate Professor has connotations that are simply not pertinent. In the UK system, something in the range Lecturer to Reader is similar, but again there is no direct equivalent.
In my opinion the best practice is to avoid translating the names of job titles. People who don't know what they mean shouldn't be judging curriculums anyway.

In the British system, Senior Lecturer would be the most likely equivalent. The teaching career ranking in the British system is Lecturer, Senior Lecturer, Reader, Professor.


text:
How to efficiently print the image of a whiteboard?
I often brainstorm research ideas on my whiteboard. I then run out of space and want to store and print the contents of the whiteboard. In general I have a system of taking a photo of the whiteboard with my phone, which is synchronised to dropbox, which then creates a copy on my computer. Now I can print the image, on my computer, but it is not optimised for printing.
It is possible to open it up in photoshop and manually make it black and white, and try to optimise the contrast and so on.
However, I'd ideally like it to be a one click process for printing a whiteboard image. The whole point is that the process shouldn't disrupt the brainstorming process.
How can I efficiently print digital photos of a whiteboard that are optimised for printing?
Naturally, the procedure might vary under different computing or phone operating systems. An ideal solution would be (a) extremely efficient, (b) minimise printing toner usage, (c) maximise readability. Useful automated steps would include: (a) optional conversion to black and white; (b) arrangement of image into a size and layout designed for printed paper, (c) optimising contrast so that the whiteboard is white and only markings print. Some form of auto-cropping might also be useful.
UPDATE: A few options I've discovered since posting:

Ricoh has a couple of Apps for iphone and Android that will email you a modified whiteboard photo. I wasn't entirely happy with the quality of the results, but with good initial lighting and black and white image, it seem to work okay. They also have a web app that is quite easy to use for uploading single files and then printing cleaned versions.
This gimp tutorial and gimp script for processing whiteboard images. The manual process if fairly straightforward, but not a single click.
Various suggestions on Photo StackExchange for getting more professional results particularly one involving shooting both the original image and and an empty white board and digitally subtracting images. It all sounds a bit complex for simple brainstorming needs.
These suggestions on SuperUser. In particular, there's an email service where you email the original whiteboard photo file and get a cleaned version back http://snapclean.me/ . It took a few minutes when I tried it.

Given that using whiteboards is fundamental to teaching and research, I hope people don't mind that I have used this site for asking the question.

"I hope people don't mind that I have used this site for asking the question" - Tools are on topic so don't worry about that. I'm interested to see the answers.

This question appears to be off-topic because it is a "boat-programming" type question that's really about photography

@EnergyNumbers I found a similar question on photography.stackexchange.com however the answers tend to focus more on the art of photography. I was thinking that academics would have more similar goals to me (i.e., efficiency) than photographers (i.e., quality).

If you can convince someone to spend money, you can get whiteboards printing built in.  My office has(had?) a few with multiple writing surfaces (switched by rolling the surface left/right) and a built in scanner/thermal printer.  You'd write on them like a normal white board; and could just press the print button when done to get a hard copy output; it would roll the screen under a scanner built into one of the side edges and make a printout as it went.

For this I use TurboScan on my iPhone.  It's designed for scanning and there are many similar apps.
It takes 3 photos and combines them to get one with good contrast and resolution.  It optimizes for readability.  It automatically detects the edge of the whiteboard and crops there; you can easily adjust the crop to be smaller if desired.  You can easily adjust contrast.
Here is a photo of what's on my whiteboard right now.  This was taken in extremely poor lighting conditions (dim, with lots of glare).  Also, TurboScan outputs a PDF, so you can zoom nicely without it becoming pixelated, but SE would only allow me to upload a JPEG, so what's below is lower quality.  Right-click and open in a new window to see it better.

Optimizing a photo of a whiteboard is similar to optimizing a scan of a page.  On Linux, I use scantailor -- it usually does a great job for what I want.  It's not automatic, but it's way faster than trying to tweak curves in Photoshop.

How much money are you willing to spend? If the answer is around $400 $900*, you can get a whiteboard capture system like this:
MimioCapture System
You would have to change your workflow to make sure your computer was up and capturing, but you use regular whiteboard markers (albeit inside the electronic case).
*educational pricing, I think, although you may have to buy additional software; I couldn't tell from the product's website
*It looks like the pricing is much more steep for a standalone system. I am not 100% positive, but it looks like the $400 system does need other expensive components. Darn. This one seems to be completely standalond:eBeam Edge

I have not seen that MimioCapture system before; it's clever. One place where I worked had a whiteboard with two screens. When you were finished with one screen, you pressed a button and it automatically printed the screen while moving over to the next screen (it took just a few seconds). I understand that some companies also use whiteboards that are linked wirelessly to the laptops or tablets, so that attendees can also interact with the whiteboard — marks that they make on the tablet appear instantly on the whiteboard, and vice versa. I guess it depends on your budget.

It would not be too difficult to set up for an "almost" one-click operation. With a little bit of Unix shell scripting you could set up a process on the print server which could do the job. E.g. you could email a photo from your phone to a special email address on the print server (to make things simple on the phone side). On the server the process could look like this:
saving attached photo upon receiving email -> processing it with e.g. ImageMagick to optimize for printing -> send to printer
P.S.
It seems the scantailor can also be used for batch processing, haven't tried it myself, though.

I wonder if there are any existing scripts for imagemagick, gimp, etc. for processing whiteboard photos.

I did see this script: http://www.fmwconcepts.com/imagemagick/whiteboard/index.php


text:
How can I secure a solo-authored paper as a PhD student, while working with a supervisor who has reputation of forcing coauthorship?
My supervisor has a bad reputation of forcing their name on papers at the final stage of research. The advisor is literally contributing zero or close to zero to my project, nothing more than- or maybe less than- very basic supervision tasks, like giving some comments on a written text.
This is unlikely to change, as the project is already approaching the final stage. How can I protect my work from being "hijacked" by an unfair co-authorship?

Does being the sole author matter much?

@AzorAhai This is a matter of principle. Ideally, no one should have their name on research they didn't contribute to. It's not out of egoism that I want only my name on the paper. I would appreciate having coauthors who would help improve the research contribution. Also from a pragmatic prespective, it's a positive signal, that I can do independent research, for whatever comes after the PhD.  A signal that I would claim, reflects the truth.

I don't know what field you're in, which is why I asked. In mine, basically no monographs are published outside of lit reviews, so having one doesn't demonstrate "independent research" because it just generally doesn't exist anymore. So the argument to your supervisor could matter a lot on whether having a monograph is much better than having a first author paper with your supervisor on it, which is the norm in my field anyway.

Be careful that you are not yourself under-estimating your advisor's contributions (Dmitry's answer is a good starting point).

If you are in a field where sole-authorship is common even when advisors contribute (some social sciences are like this from my understanding, for example) then that advice may differ.

@AzorAhai I can testify that in some countries and fields, solo-author papers (and papers in which one is the most senior author) are relevant for hiring and tenure decisions.

@lighthousekeeper Yep, that's why I brought it up!

Just as a clarification, I am in the field of  social science. So, many aspects of the "Lab Culture" may not be necessarily relevant in my case.

Only way is to do separate independent work by yourself and try and publish it on the side, many people have done it.

@Tom: It agains tends on the advisor. Some (extremly bad) advisors have a policy "whatever my student writes, I must be coauthor or they cannot get their phd because I'm in power".

Yes, that is very unfortunate.  I think in reality if you are in that situation there is not a whole lot you can do, perhaps raise the issue to someone higher up if a case can be made that you are the sole author?  If I were a PhD supervisor I would in fact encourage my students to try and publish things by themselves if they are capable as that shows independence.

Related: How to find out whether my advisor expects to be author of a paper to which she did not contribute? (probably does not help you but others in a similar situation).

Don't put the cart before the horse. Ideally just try to do the best research you can, and be open to using the guidance of the people around you to help you towards that. Refusing all help/guidance for fear of diluting authorship is unlikely to help you, at any stage in your career, but especially when you are very junior.

@Hussin “Also from a pragmatic perspective, it's a positive signal, that I can do independent research […].” That's likely a non-issue. You haven't clarified whether co-authorship is common in your field or not (“social science” is awfully vague) and seem to have very strong feelings about fairness and the contribution of your advisor but if we are purely pragmatic, being the first author is what counts. In most fields, nobody will think that having co-authors means you're incapable of independent research and nearly everybody you will compete with will be in the exact same situation.

Does your superviser deserve an authorship? Check the following:

Have they contributed to the research design, in form of suggesting a topic to investigate, advising on methodology, suggesting literature?
Were they involved in evaluation of results, in form of checking them and contributing an opinion on whether the work is going in the right direction?
Have they contributed to writing a paper, in form of contributing an introduction or abstract, or editing the manuscript?
(*) Have you used any of the facilities or financial streams (e.g. stipendship) funded from your supervisor's research budget?

If any of the above is true, then your superviser may actually deserve an authorship.  You can also check Nature Authorship Guidelines or a similar document in your university.
If you answered no to all of the above, then it is absolutely appropriate for you to publish on your own. Simply use the Authorship Guidelines to politely explain to your supervisor why you believe that they should not be included as an author. You may want to discuss your position with a dedicated unit in your University/Department, such as Research Office or the Head of the Department.
UPD: (*) As many people commented (and I agree), criteria (4) is controversial. In many areas providing funding on its own does not qualify for an authorship (see e.g. Vancouver protocol). However, in many departments it is a norm to always include the Head or Director of the Lab as the last author, and it may not be easy to challenge this agreement for a PhD student, particularly if you benefit from this funding.

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Sadly, it may not be possible to do this and also get your degree. If the supervisor needs to sign off on your graduation and/or dissertation, then they have sufficient power to end your career before it starts, or at least delay it while you find a different advisor and maybe a different institution.
I hate to keep giving this advice, but it may be your best course to go along and complete your degree so that you become independent of his influence. Once you are free you can control your own career.
An alternative, not recommended, is to complain up the chain of authority and hope you reach someone who cares enough to help you. But you imply that this has been going on, so finding that person seems unlikely.
Prioritize your long term goals, not this one paper. It is still positive for you to have a publication, no matter the other issues.

The real problem here is that the supervisor has a bad reputation.  If you only complain and do not get a new supervisor, the result is their reputation will be worse, and they will still be your supervisor.

The advisor is literally contributing zero or close to zero to my project, nothing more than- or maybe less than- very basic supervision tasks, like giving some comments on a written text.

Your problem is that you are not being advised. You can publish whatever paper with whoever as coauthors, nobody can stop you. But if you are in a program at an institution and you are expected to receive guidance, you should solve it.
You are not expected to have no advisor, that is bad situation to be in, especially during PhD training. Seek help.
Talk to your department and your academic advisor. For example, at USC they say clearly:

The office of Viterbi Admission and Student Engagement (VASE) provides services and resources to help students in the successful pursuit of their graduate degrees.

"nobody can stop you". In theory, of course not, but a bad advisor can definely do so (or at least make your life bad if you don't follow).

@user111388 i tried to highlight the real problem of the OP. Of course, there is nuance

I will add to Dmitry and Buffy's excellent answer to point out the following.

You say "The advisor is literally contributing zero except [...] giving some comments on a written text."

In my opinion, this makes them a co-author. He or she do not have to have physically edited the document themselves to add material or sections you had not considered, in order to be defined as an "author". In fact, I would argue that a supervisor's role in a paper by their subordinates is exactly that: to make corrections and suggest changes. Now you may disagree with respect to how important those comments were in terms of shaping the form of the final manuscript, but this then becomes more of a "how many hairs make a beard" distinction.

"My supervisor has a bad reputation of forcing their name on papers at the final stage of research". As long as point 1 above stands, they have every right, and would probably feel that you robbed them of their contribution towards this project if you attempted to remove them as an author. Remember that their contribution started way before 'corrections on the manuscript' took place. It started when you two sat down to discuss how the project should be carried forward. Any research that formed part of the manuscript which resulted from your collaboration and those discussions make him or her a valid co-author. It would have been a very different scenario if you thought of something by yourself at home and an old professor suddenly knocked on your door and demanded their name to be put on the manuscript out of the blue.
"How can I protect my work from being "hijacked" by an unfair co-authorship?". My final point is a practical one. What you consider as 'hijacking' may in fact be 'saving' your manuscript. I don't know what the norms are in your country, but in most international labs, it is common for work to be associated to the lab it came from in terms of forming a judgement about its quality, rather than the first author, unless the first author has managed to establish themselves enough in the field to be a recognizable name. I have worked with people who would refer to names via the lab rather than via the author, and would be more willing to read a paper if they knew it came from a reputable lab, and less willing if it was from a single unknown author. So, make sure that you don't shoot yourself on the foot by insisting the lab leader is excluded from the paper. It is generally in your best interests to co-publish a paper along a person who carries some weight in the field (not to mention you would be burning bridges with this person for all the wrong reasons).

Having said all that, it seems to me that the problem here is less whether your supervisor should or should not be an author from a technical point of view (though I believe it sounds like they should), but the fact that you two seem not to have the best relationship, and that this is affecting your psychology and ability to perform work in a calm manner. Now this is an important issue. One's relationship with their supervisor, for better or worse, is one of the most important factors for successfully completing a PhD, let alone getting something useful out of it, be it skills, a professional network, etc.
So, perhaps you should be focusing on the more general picture, i.e. what you could be doing to improve your relationship with this person instead, or considering a change in supervisors, adding a co-supervisor, or taking measures to protect yourself from malicious actions (assuming they're that kind of person, which I did not necessarily get the impression they are).

Can you include your field? In my field, it is common that collegues (supervisors or not) give comments on a paper. Yet, most of the times they are thanked in the acknowledgements and not an author. It's definitely not true in my field (maths) that everyone who gives comments (referees also in your field?!) becomes coauthor, especially this statement is in my field not followed by "Period." as if it was a law of nature.

@user111388 thank you for this comment. Indeed. I meant this in the context of PhD supervision, and in terms of comments / discussions that have guided the flow of experiments / manuscript. (My fields cover medicine, computer science and engineering). But I can see how this process may differ in maths (which tends to be a less "lab-based" discipline anyway). It is true that a passing suggestion by a random colleague which serendipitously happened to bear fruit would not be appropriate grounds for co-authorship, but I hardly think this is the situation here in the context of PhD supervision.

Thanks @TasosPapastylianou I am working on economic research. Your answer has several fair points. However, many of the norms in lab research may not apply in my case. As mentioned by user111388, it was the first thing that came to my mind, that seminar participants, and above all referees in peer review, usually contribute comments that even lead to improvements the paper, but it doesn't make them eligible for coauthorship. But everyone is thanked in the acknowledgement.

Thank you for your insightful comment. However, could you as a compromise delete "Period."? I do absolutly not think that it is so clear-cut, even if advisors.

@user111388 done :)

@Hussin It is ultimately up to you to decide where in the spectrum your particular circumstances lie. I think if there's anything to be gotten from the above discussion(s), is that it's worth considering that there is a spectrum of opinion, where you possibly thought there might not have been. And that it is highly likely that your supervisor is not approaching this from the point of view of a 'disney villain', but possibly feels they rightly deserve and should be listed as an author. In which case, subjective 'fairness' is not the only criterion: you also need to weigh up the cost of 'war'.

As for the distinction between the role of a supervisor and chance-suggestions by reviewers or colleagues, I would say that this is comparing apples to oranges. The role of a reviewer is not to help you shape the research; they are simply acting as a good-faith proxy on behalf of an editor. Similarly, conference participants enter in good-faith dialogue, but do not expect to join your research activities. Your supervisor on the other hand holds a position of responsibility to you as a phd-student, ensuring guidance for fruitful research and expecting some recognition for helping shape the work

My supervisor has a bad reputation of forcing their name on papers at the final stage of research. The advisor is literally contributing zero

You need a new advisor.  If your advisor has a widespread bad reputation, that will hurt your reputation.
As a side effect, a new advisor is likely to also contribute effectively and follow ethical standards for authorship.

I did not interpret "having a bad reputation of forcing their name" to be equivalent to "having a bad reputation in the field" more generally. I simply took it to mean this person has a reputation internally in their lab, among the other students, of pulling their weight and insisting their name goes on the paper, even when the students feel otherwise. If they also have a bad reputation in the field, then yes, I agree 100%.

@TasosPapastylianou you are right. It's more of an internal reputation of a norm that students have to "live with". Not that the supervisor has a bad reputation among the scientific community.

Academia is a small world, surely word of his poor 'internal reputation' must get around.  Try to change to a new advisor if possible.

@Tom: I disagree. There are a lot of famous people who are abusive against students, but among researchers this is viewed as "funny quirks of geniuses" or at best "it's the student's institution's problem, for all we know it's a great scientist".

If possible try to change to a competent supervisor is my only advice in that case.  A person could be great at doing research and be incompetent as a PhD supervisor, the skills required are not the same.

@user111388 I strongly disagree.  Abusive advisors are from time to time, and should be, banned from advising.  "funny quirks of geniuses" is Hollywood nonsense.

@AnonymousPhysicist: They should be banned from advising, yes. They are only rarely. If done, it is because the university does something (which happens very rarely and mostly only because there is threat of eg making cases public) and not because of reputation among collegues.

@user111388 It varies.  At some universities, academics are banned from supervising PhD students because they did not reach their performance targets (books published/year).  For every public case there could be many you do not hear about.

If I were you, I would not be trying to stick to your principles but ended up on your supervisor's bad side for the rest of the duration of your Ph.D. and beyond. You have to play the long game. Stop obsessing with the authorship of this one or the next couple of papers. Sharing one or two papers with your supervisor is not going to harm you. In fact unless your supervisor has only bad reputation in the field (in that case I don't know why you picked him to be your supervisor in the first place), it is going to help your career. Not sharing is going to hurt you in the long run for sure!

Further to this point, since you don't want to make the career harder, maximise the involvement of the supervisor who will be an author of the paper. Send them the entire paper and get feedback from them. Or send them the abstract and get them to edit it (pop in a deliberate minor mistake, e.g. a typo, to ensure that you get them involved).

Different fields have different customs, norms, and guidelines. An answer valid for Mathematics would not be valid for Computer Science or Physics. In Computer Science, realizing that there is a problem to be solved or that there is an application for a certain methodology can be sometimes enough to justify co-authorship, even if it appears that the actual work was done by others.

The premise of the question is that the supervisor is no coauthor by the field's standards, I think.

I'm a computer scientist, and I don't think either of the things you suggest is even close to sufficient for co-authorship.