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My research area is Computational Biology. My work involves in silico methods, I do not carry out any wet lab related experiments. My supervisor wants 4 chapters (apart from introduction and conclusions) for my PhD thesis. He said each chapter should be a journal paper (must be SCI indexed, with no article processing charge (my institute does not pay for APC's, and the APC amount is equal to my 3 months fellowship, hence paying APC alone is also not feasible) and above Impact Factor 2). I already have made a review paper, but that goes into the introduction. Hearing his demands I am a bit scared that I might end up doing PhD from 5 or 6 more years, and I do not want to do PhD for 7 8 years. I am in my 3rd year right now. He told me this after 1.5 year of joining. I do not think I will be able to give 4 more journal papers in the next 3 years.

My current work status is, that I am working on 3 papers simultaneously now. One work is 70% complete (can't say it is totally complete unless it gets accepted by a journal). Another work is 50% complete, and the third I have just started.

My questions are:

  1. Do you feel that the demand of my supervisor is too much?
  2. Is it even possible to produce 4 more journal paper in the next 3 years?
  3. Is it possible to bargain the count of paper down to 3 instead of 4? If so, how should I do it?

Note: The advisor's rule is the institutes rule, the advisor has the last say in decising whether I get my degree or not. Many people from our institute graduates with just one journal article too.

  • This certainly seems more feasible for computational biology compared to, say, molecular biology where the scale of projects and papers can be 2+ years. It's hard to say if your supervisor is demanding too much without knowing the kind of work you are doing. I don't know how far along you are or where you study, but your thesis committee should provide some counter-balance to your supervisors demands. In my experience, most supervisors seem to compromise with their colleagues when it comes to the requirements for your dissertation. – syntonicC Sep 25 '16 at 19:27
  • Your "note" is confusing. Do you mean to say that the advisor's rule is NOT the institute's rule? – BMD Sep 26 '16 at 4:06
  • @BMD i have edited the question – girl101 Sep 26 '16 at 4:17
  • The requirement of a journal without APC makes no sense. Many, if not most, of the top computational biology journals are open access and have APC. – Bitwise Sep 26 '16 at 6:58
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    If you have 1 paper at 70% complete, and a second at 50%, and a third just started, so let's say 5%, then that adds up to 1.25 papers. So you don't need 4 papers in 3 years, you need 2.75 papers in 3 years. I know you haven't gotten any of the papers pushed all the way through to publication, but don't discount the work you've done so far. How much more work will it take to push that 70% paper out the door? Getting that first one published might help your confidence at least. – user137 Sep 26 '16 at 13:05
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Do you feel that the demand of my supervisor is too much?

I work in theoretical mathematics. In that field, a requirement of four publications in journals of impact factor greater than 2 would stop more than 99% of students from getting a PhD thesis. (I got my PhD in 2003 and am now a tenured, "full" professor. If I'm not mistaken, I have zero publications in journals of impact factor greater than 2....but in my field we do not speak of impact factors when we talk about journal quality.)

The above paragraph is there only to tell you where I'm coming from. In fact I do not understand the logic behind such a requirement -- in particular, I don't see where the number four is coming from, and if I wanted to impose high standards on my students I would do it in terms of the quality of their work rather than the quantity. But I can't say that the demand is too much, since I am not in your field, am probably not in your country or university, and I am not working with your supervisor. Whether it is too much is mostly up to the two of you to decide, along with other members of your committee and subject to the rules of your program and university.

Is it even possible to produce 4 more journal paper in the next 3 years?

It is certainly possible for someone. I would be willing to bet at any reasonable odds that there are students in computational biology who have this many publications in this amount of time. I urge you to look in the literature of your field and see when, where and how often this occurs.

Perhaps you mean to ask whether it is possible for you. That's a really good question, though of course we are not in a position to answer it.

Is it possible to bargain the count of paper down to 3 instead of 4? If so, how should I do it?

The language of "bargaining" is not very apt, but: yes, you should certainly discuss the situation with your advisor sooner rather than later. Your advisor is setting what I think we can agree is an unusually high bar -- you mention that other students in your institute have gotten their PhD with a single paper, and he is asking for four papers. Note though that you said that that's what he wants. Many thesis advisors have high expectations for their students and try to push them to do their best work. (And the others are not very good advisors, in my opinion.) However, (i) what you want your student to do, (ii) the least they need to do to graduate and (iii) what they actually end up doing are three different things: wildly different, sometimes. Here you seem to be assuming (i) and (ii) are the same. I think that they probably are not, but they could be in your situation. The only way to find out is to ask.

Here are my specific recommendations:

Step 1: Do your research. Find out the publication records of students in your area. In particular, look at all the students who have gotten PhDs in computational biology in your institute and under your advisor. Then pick a few other institutions for comparison, including at least one that would be regarded as better. How often is it that students have four publications in IF > 2 journals before they graduate? If this happens only a small percentage of the time and/or if it almost never happens at your institute or with other students of your advisor, that's a strong clue that the constraints you've been given are aspirational...or ought to be.

Step 2: Have a serious conversation with your advisor. Show him the research you've done in Step 1 -- not confrontationally, but so that both of you will be working with the same facts. Then show him a plan of the work that you will do and the papers that you will have published by a certain time. This plan should be serious but realistic: you should be able to defend the amount of time you'll spend at any stage. Your plan should include a specific time that you want to graduate. If your plan shows you with three papers for sure and very iffy on the fourth, bring that up explicitly with your advisor.

I think it is likely that you will find that your advisor is flexible on the requirements and appreciative of the thought you've put into your future. However, it is also possible that he is absolutely intransigent and insists on more papers than you think you can reasonably write in the allotted time. Well, if that is the case, far better to have that information now rather than three years later! If you have it now, you have plenty of time to figure out how to respond to it.

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    +1 for pointing out that an advisor's stated goals for a student may not be what they'll be satisfied with. – Kimball Sep 25 '16 at 23:30
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  1. Purely opinion.
  2. Possible, yes. Guaranteed, no.
  3. You should not bargain. You should follow your university's procedure for evaluating doctoral theses. Your advisor's job is to advise you on what should be in your thesis. If he is ambitious and you do as he suggests, it will make both of you look good.

I have often observed that if the PhD student is offered a good job, suddenly everyone realises they have written a good dissertation. Publishing and getting a job offer are both ways to show evaluators you are ready to graduate.

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    I agree, but these demands are somehow ridiculous. Of course, I don't know this field, but in physics the basic requirements for a PhD is at least one paper published. Although, many prestigious universities do not have any such requirements. Searching through history, in the past many respectable physicists today have obtained a PhD with only one or none papers published. – Mikey Mike Sep 25 '16 at 12:39
  • Depends on topic and university and group. There are world-class groups with few publications. Question is: did the candidate know that beforehand? Or are they only being told now in the mid of their thesis? Perhaps the results are promising? – Captain Emacs Sep 25 '16 at 12:46
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    I downvoted this because it is one-sided. Sure, if the supervisor has high expectations and the student meets them, then everything is great. But you have failed to allow for what happens if the student does not meet them. If we take this supervisor at his word, if the student is only able to produce 3 papers, they will not graduate, even if that would be perfectly adequate for a good thesis and a good job, and that probably isn't a good outcome. – Nate Eldredge Sep 25 '16 at 13:40
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    As to #3, maybe "negotiate" isn't a good way to put it, but the student does have agency. You seem to be proposing a relationship in which the advisor is always right and the student should just do as they are told. I disagree with that. Note that at many places, the "university's procedure for evaluating doctoral theses" is effectively "advisor decides unilaterally whether it's good enough", so in such cases that sentence doesn't add anything. – Nate Eldredge Sep 25 '16 at 13:44
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    @AnonymousPhysicist: Well, I don't seem to be the only one who drew that inference, so perhaps you would like to edit your answer to clarify. – Nate Eldredge Sep 26 '16 at 1:24
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Though it may be difficult, 4 papers isn't impossible for computational biology, depending on the content.

In computational biology there is really a wide variety of paper types - experimental, computational modelling/analysis of data, completely theoretical. Some papers are even focused on just describing tools. The requirement of IF>2 is very low for this field. As an example consider the journal PLoS ONE which has IF>3 and will accept any paper regardless of perceived importance as long as there is some minimal novelty and it is technically sound. So I suspect the idea is to go - in the worst case - for quantity rather than quality (e.g. salami slicing or least publishable unit). Personally I am not a fan of this way of publishing but there are many who adhere to it, and I can understand why. I am guessing that the supervisor thinks this way is better for you. This way you have a good chance to get several publications, but if you put everything together into one paper in order to get it into a prestigious journal, there is a chance that paper will not be accepted or will only be accepted into a bad journal, and that could mean trouble.

So, for example (though a bit extreme in my view), If you have an idea for a new bioinformatic tool, you could write one paper just on the theoretical part (maybe with some simulations on synthetic data), a second paper on applying it to biological data and correlating with other biological datasets, and a third short paper on the tool itself (maybe you set up some website/server etc).

Of course the best thing is to get 4 landmark papers in prestigious journals, but I wouldn't count on that...

  • Note that the advisor knows about the Plos's shortcut to publish in a journal with an IF above 2 since the request is without article processing charges. Clever. – Cape Code Sep 26 '16 at 6:04
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    @CapeCode hmm, that restriction is very odd, given that most of the top journals in this field are open access and have APC (e.g. PLoS Computational Biology, Molecular Systems Biology, Genome Biology). Regardless, IF>2 is still not very difficult to pass (but of course the whole IF thing is kind of silly). – Bitwise Sep 26 '16 at 6:52
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It depends on what you want to do after your PhD.

If you're interested in getting an industry job, then I think that it's reasonable to try to bargain with your supervisor to try to cut down on his/her demands. I don't want to live like a grad student for 7-8 years/I can't survive on a grad student stipend/I just want to get out with a degree are all reasonable arguments (if properly and politely worded).

If you want to continue on an academic path, then I recommend that you follow your supervisor's rules. Sure, you can still bargain, but remember that your supervisor's recommendation letter is what will get you your jobs for the rest of your career. If all of the other students of your supervisor follow his/her rules, and you whine about not being able to fulfill your supervisor's expectations, can't you guess what will be written in your recommendation letter?

  • Also, if the supervisor is known to set high demands, a good recommendation letter will carry a lot of weight. – Patricia Shanahan Sep 25 '16 at 16:54
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    "I don't want to live like a grad student" is not bargaining. Begging, maybe. – Anonymous Physicist Sep 25 '16 at 21:25
  • @AnonymousPhysicist Ha! Hence the "properly and politely worded" caveat. – BMD Sep 25 '16 at 21:37
  • @BMD my supervisor has himself agreed that his recommendations don't work in many places.... – girl101 Nov 5 '16 at 4:28
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Check with your university Ph.D. degree section, and ask for the requirement. If the papers are required as chapters. Then it's your mistake that you did not read it on joining. If the papers are not required as a chapter in the thesis instead you have to write the chapters, then you can talk to your supervisor in a nice way that since the papers as a chapter is not a requirement for a thesis, so lets come to some mutual conclusion.

  • Have checked, it says, depends on the advisor and the PhD committee's opinion combined .. – girl101 Sep 26 '16 at 7:41
  • There should be a manual, i guess it is not the choice of supervisor. As in my area some public universities has publications requirement and one of my friend has 13 q1 journal publications in three years. While in my univeristy we dont have the publication requirement and a supervisor can not just ask you to do. He also has to follow the quality manual that is given to students and profs. ask them to show you in written that its the decission of supervisor. – Shahensha Khan Sep 26 '16 at 9:15
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To work out what is reasonable in your field, look up the CVs of recent graduates in your field, who have attained the type of position that you are aiming for after graduation. How many papers did they publish in their first few years, and where?

I'm not a computational biologist, but am in the related field of ecological modelling. In my field, 4 papers in 3 years would be a low-average benchmark for a working academic and a moderately high benchmark for a PhD student, but should be achievable by a strong student with good supervisory support.

Some journals you could aim for include Bioinformatics, Ecological Modelling, Applied Mathematical Modelling and possibly Environmental Modelling and Software. I'm sure you are aware of others more specific to computational biology that meet your advisor's guidelines.

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