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Barb Bryant
ISMB2010: Barb Bryant
PLoS Session on How to Write a Good Paper
July 13, 2010 - Comment - Share
Phil Bourne and Steven Brenner are presenting for the first hour, 10:45-11:40. - Barb Bryant
Having published good papers consistently counts for at least 50% of career advancement. - Barb Bryant
(Phil only published 2 papers in a 10-year period while he was leading the PDB. That was a big mistake for traditional career path, but he wouldn't have done it any different way. It was an issue when he came up for tenure.) - Barb Bryant
Other things that matter in an academic career: Teching/mentoring, gratns, community service, good talks and networking. - Barb Bryant
Steven: For a young scientist, papers matter even more. - Barb Bryant
Steven: When I'm looking at a postdoc or junior faculty applicant, I look at where they trained, who their advisor was. I look at what papers they were first author on. Then, is there any paper that is a real standout and important. Then, how many papers, and what is their nature. - Barb Bryant
Andrej: what your rmentor says about you makes a lot of difference too. - Barb Bryant
Alan Turing - signal processing. At AT&T he gave a talk that was never published; we attempted to reiterate this in a recent PLoS CB paper: 2007 3(10)e213. - Barb Bryant
Phil: Work only on important problems. Work with important people. You have to figure out for yourself what is important. - Barb Bryant
Do this when you're young. - Barb Bryant
You need more than brains: you need courage. The system is not well geared for (especially) young people to take risks. Risky papers are often rejected. We're beginning to see evidence of how the review system fails. The review system supports incremental work better than risky, outstanding work. - Barb Bryant
Take PLoS ONE. PLoS ONE was intended to be a place to put work that may not be enormously innovative, but it is sound. But what has happened is that it got a number of risky papers, some of which have turned out to be important, and highly cited. So this journal that is supposed to be at the lower end of things, has a relative high impact factor. - Barb Bryant
Steven: Examples. Original paper where we wrote about the SCOP database. Very highly cited. Rejected by reviewers; my advisor battled the journal to get it published. My arguably most important paper, identifying targets of nonsense-mediated decay, was rejected by three journals. Most-cited paper in field of alternative splicing or nonsense-mediated decay. Don't be discouraged! If it's important, it will eventually be recognized. - Barb Bryant
Phil: The PDB paper has been cited 10,000 times. Noone has ever read it... - Barb Bryant
Luck favors the prepared mind. - Barb Bryant
Time management is critical. The amount of time in the lab doesn't necessarily translate to productivity. You don't get taught how to manage your time well. Read books on time management. - Barb Bryant
Work from your heart. If your heart is not in it, you won't succeed. You need the passion to go the extra nine yards to do a great piece of work. - Barb Bryant
So all of that was prerequisite to writing a paper. Now, how do you do it? - Barb Bryant
Start writing the paper on Day 1. - Barb Bryant
Draft paper helps focus the work, makes sure that you write it up; is easily shared with colleagues for feedback that can help you with the work itself. - Barb Bryant
Steven: another reason to have it written up early in draft form -- I ignore "in preparation" on a resume. If they say "in preparation, draft available", that makes an impact if I can see the draft. - Barb Bryant
Steven: another reason to write the introduction early: "A month in the laboratory can save you an afternoon in the library." Being forced to write the introduction might help you find previous work that will change what you do. - Barb Bryant
Phil: If you hate writing, get over it. If you do not write well, take classes. Now. - Barb Bryant
? I wonder if they have suggestions for people who just don't have good command of English -- what about working with a writer, etc.? - Barb Bryant
Try to see your paper as the reviewer will see it. Try to look at it "from a distance." - Barb Bryant
It might be motivating to you to realize that the paper is going to be your (scientific) legacy, long after you're gone. - Barb Bryant
Some ingredients of a good paper: novlety, good coverage of the literature, good data, strong statistical support, clarity of presentation, thought-provoking discussion. - Barb Bryant
Look at the scope statements of the journal you're thinking of submitting to. - Barb Bryant
Don't rely on your PI to tell you the novelty of the work - figure it out for yourself. - Barb Bryant
In discussion, guide people to build on the work. - Barb Bryant
DON'T try and prove that you are smart. - Barb Bryant
Avoid the kitchen sink syndrome = putting too much that is not relevant into the paper. - Barb Bryant
Maintain a good bibliographic database (EndNote, RefWorks, etc.). Consult a citation index (ISI, Google Scholar); consider using that to annotate your database entries. Use a tool like Mendeley to store annotations. - Barb Bryant
(Mendeley is a way of annotating PDFs; you can share annotations.) Explore social bookmarking to find out what others have been saying about papers. - Barb Bryant
Q: how important is the citation index of a paper? A: not important. What matters is how good and relevant the paper is. - Barb Bryant
In 2000, Phil wrote a paper on alternative views of looking at protein space. For 5 years, noone cited it. But then it became a hot topic and citations started to pick up. - Barb Bryant
Steven: There is a tendency to have a winner-take-all approach. Everyone will cite one paper, even if there is a more relevant paper. It's important to go out and find out which papers really are most relevant. - Barb Bryant
Steven: Have your whole lab get together and pick one program to store your data. Even if it's not the best program, being able to share the tool is really valuable. Phil: we lack good project management tools that map to the scientific endeavor to allow us to share and maintain output from the lab. Come talk to me about developing a company around this... - Barb Bryant
Phil: Have colleagues critique your paper. - Barb Bryant
Become a reviewer early. Shadow more senior people in reviewing. Look at the other reviews of the paper. - Barb Bryant
Approach program committees of conferences. - Barb Bryant
Hold journal clubs. Identify good and bad papers in journal club and elsewhere and study tehm. A good paper will likely tell a story and be enjoyable to read and follow. It's pitched at the right level for the intended audience. - Barb Bryant
Acknowledge the people who submitted the review. - Barb Bryant
Q: will the program committees and journals accept volunteer reviewers, or do you have to be asked? Steven: There are two ways this can work. First, a PI can invite a student of theirs to help review it. Second, if I can't review it myself, I can recommend someone in my lab to do the reviewer completely themselves. The editor then can choose whether to use this student/postdoc reviewer. - Barb Bryant
Choose the journal wisely. Do you read that journal? Do you cite it? Is it a top-notch editorial board? Does it have highly accessed papers? What is the rejection rate? What is the average time to publication? (Find out by talking to people who have published in that journal.) Is it indexed in PubMed? - Barb Bryant
And, most importantly, does the scope match your work?? - Barb Bryant
Use the presubmission inquiry if the journal has one; it helps in determining scope. - Barb Bryant
Mark: what emphasis to place on how highly cited the journal is? Phil: I don't care anymore at my point in my career. This is my personal opinion. The review process is quite broken. But others judge job candidates by this. What do you think? - Barb Bryant
Mark: shouldn't think about impact factors. - Barb Bryant
Phil: Other communities do not have a review process, but a moderation. Then it is how much it is accessed by the community is the judgment of its worth. - Barb Bryant
Steven: You need to think about who will be evaluating you in your career. Traditionalists will care about which journal. If you are looking for a job right out of post-doc, won't have time to have gotten citations on the paper, so which journal matters more. It helps to have letters of reference that describe the importance of the work. - Barb Bryant
It helps to understand the editorial process. - Barb Bryant
Know that the best scientists get rejected and/or have to make major revisions. - Barb Bryant
Post-review phase. Again, "get over it". Buckle down and do the work. Don't be defensive. Address every aspect of the reviewers' concern. It's fine to disagree with a reviewer, but have the conversation, don't shy away from it. Make it clear how your revision addresses the reviewers' points. - Barb Bryant
Examples of a good paper and bad paper... No time to do this... - Barb Bryant
Steven: Bear in mind that the reason we do science is to create new knowledge and contribute that to the body of scientific knowledge. You do that through your papers. So papers must be an effective conduit. - Barb Bryant
Steven: Ability to communicate is key. Most of us are not great writers. You need to figure out what works for you. Team writing can be very effective. Example: one student had to talk it through first. - Barb Bryant
Share it with colleagues before sending it out for review. - Barb Bryant
Make sure you make it easy for the reviewers. Example: when you make a revision, make it clear what you changed. - Barb Bryant
Figures. When people flip through a paper, they usually look at the figures first. You should invest major effort in getting the figures perfect. You might revise a figure 100 times. I have people in my lab take a course in the visual presentation of information. - Barb Bryant
Steven (still): it's important to make sure that you are right. If you have 10 papers and one has a major flaw, that can be devastating. - Barb Bryant
Surya Saha - just finished PhD and starting post-doc. Has these questions from first-time authors - Barb Bryant
(We are going into the second half of the workshop, with a panel of 7 people) - Barb Bryant
Surya: what happens inside the editorial process of a journal? - Barb Bryant
Nils Gehlenberg - student. Pros and cons for new authors of supporting alternative publishing and evaluation models. - Barb Bryant
Article metrics. At yesterday's future of scientific publishing - I can influence citing in blogs and social networking sites. Should I go out and market my papers? - Barb Bryant
What about publishing that are not papers - like data, or software tools? Will that look good on my resume? - Barb Bryant
Mark Gerstein (experienced author): Scientific publishing in the future. - Barb Bryant
We are seeing a distinction between databases and journals getting blurred. People are approaching reading like databases -- you query for an article. Also, people read database entries, e.g., to find out about gene function. - Barb Bryant
It's hard to fit everything into conventional journal articles or biological databases. Why are people citing SCOP so much (for example)? Are they *reading* it? Or is it associated with a piece of code or database that they're using? The latter, often. - Barb Bryant
People cite a paper not because they read it but because they saw an easy-to-read summary or someone cited it in a lecture that they saw. - Barb Bryant
Mark's view: We can update scientific publishing; make it more multi-tiered, more compatible with the digital world. I advocate a structured digital paper. It's not a single narrative, but a set of streams of information - some computer-readable and structured; one or more stream for the human reader. - Barb Bryant
You do this not as separate from the paper publishing, but as part of publishing the paper. - Barb Bryant
Structured abstract. Structured digital table. (Are examples) - Barb Bryant
Chris Sander speaks next. - Barb Bryant
We have a project: the Factoid Project. - Barb Bryant
Factoid Project: require authors to submit basic facts they've derived to a database. - Barb Bryant
Scientific publishing needs to be revolutionalized. - Barb Bryant
We need to take away power from reviewers and editors. - Barb Bryant
We should engage in marketing our papers (though prefer a different term) - Barb Bryant
We should change how papers are evaluated by potential employers and tenure committees and so on. - Barb Bryant
Talks about figures with (A), (B), (C), and having to find the letter in the caption. Figure captions are hard to read and understand. In Time Magazine, you won’t see those. Appeal: make figures an integrated information panel. Let’s put together a small working group; write up an opinion piece, send it to journals and ask for a change. I’ll help. - Barb Bryant
Chris proposes another working group about assessing a paper’s impact and the author’s contribution. - Barb Bryant
Chris: Doesn't like PLoS Computational Biology because of the goal of increasing the rejection rate to improve impact factor. Optimize scientific contribution not rejection rate. - Barb Bryant
Chris: How your papers get advertised. You can promote your own work. Don't just rely on the editors. Don't just rely on the reviewers. Don't rely on the paper coming out and someone maybe reading it and citing it. Coming here and doing posters. - Barb Bryant
Gary Benson: Professor at BU; editor at NAR. Edits web server issue, an annual special issue. - Barb Bryant
I like papers, says Gary. I like looking at figures. I like when people put a lot of effort into organizing their thoughts. I like it when people use examples in their papers. - Barb Bryant
narwbsrv@bu.edu if you're interested to submit a paper. - Barb Bryant
In Comp Bio, people make predictions about something. It's easy to make predictions; it's not easy to validate them. At NAR, we have a strict policy that you have to show considerable evidence of validation, with data that was not used to develop the model you're presenting. - Barb Bryant
Pitfalls for journal submission. - Barb Bryant
Prior publication: Arxiv is an archive; that is not considered (by NAR) a citable publication, so it's OK - would not exclude your article for that reason. On the other hand, we saw a paper previously appearing in PLoS Currents -- and we do consider that a prior publication because cited in PubMed. - Barb Bryant
Conference submissions are prior publications in some cases. Conference proceedings can have fairly large papers, and are usually citable. - Barb Bryant
Open access: this is a journal's way to compete with online repositories. It's a way to make your paper free to everyone. All publishing should be like that - but it costs money. Authors have to pay usually, for open access. - Barb Bryant
The review process at NAR: Senior editor evaluates for meeting scope. Pass it on; next editor again considers scope. If that passes, then get reviewers. Authors are asked to suggest reviewers. If you propose reviewers, pick people who are not your friends but are knowledgeable in the area. - Barb Bryant
We pick 2 reviewers. You appreciate as an editor getting suggestions for reviewers. I usually respond positively to volunteer reviewers. - Barb Bryant
Reviews usually take 2 weeks at our journal. Some are good, some are not. You want more than a paragraph! Then the editors try to make a judgment based on those reviews. If there is disagreement the editors will seek a third review, and this can take additional time. The editor usually informs the author of this delay. - Barb Bryant
We try to have a 30-day turnaround time. Then if the reviews are positive, you get a chance to modify your paper, and our goal is 60 days. - Barb Bryant
Be non-confrontational in your letter responding to the reviewers that accompanies your revised manuscript. This is a dialogue between you and the reviewers, monitored by the editor. - Barb Bryant
End of Gary's introduction - Barb Bryant
Andrej Sali speaks next. - Barb Bryant
Presubmission inquiry - the editor is looking both at scope and at quality. It's important to put effort into this. - Barb Bryant
Suggested reviewer lists: I found through experience that it is difficult for authors to predict which reviewers will be fair or supportive, or negative. You may think someone is your friend, but they are not always your friend. Don't put too much attention onto who you think is your friend. - Barb Bryant
Phil will put his slides on the PLoS CB website; Andrej thinks that’s great, and he’ll be requiring people in his group to go through them. - Barb Bryant
Try to satisfy reviewers. Why not? Obviously, you want to do what you think is right scientifically, so do not compromise that. - Barb Bryant
Collect common wisdom within your lab about writing. In my (Andrej's) group: definitely start with written document on Day 1. Outline the manuscript before you start the project. Keep it up to date as the process goes on. Keep in mind the key idea - why should people read it? Summarize that in the title. No more than 2-3 sentences on the main message. - Barb Bryant
On to Alfonso Valencia, editor of Bioinformatics. - Barb Bryant
What to publish: your work. Where to publish: Bioinformatics, obviously. :-). When to publish: not before my holidays. - Barb Bryant
There is both opportunity and risk. Consider the music industry: the web has had a huge impact; musicians aren't sure how they are going to survive. Newspapers too - huge changes. - Barb Bryant
The web affects not only science reporting but science production. - Barb Bryant
People who have already built a solid scientific reputation can afford to try out and champion new modes of publishing. Young scientists have to be much more careful so as not to harm their career. - Barb Bryant
Not all papers are equal. Application notes are different than scientific papers are different than discovery notes. - Barb Bryant
It's more important to be able to build on a paper than to reproduce the paper. A good paper enables more research. - Barb Bryant
Publications are an essential instrument not only for knowledge distribution but also as a tool for organizational decision-making: evaluation of institutions, grants, fellowships, positions. - Barb Bryant
Before replacing impact factors, think: with what? - Barb Bryant
You don't have to do all that the referees/editors ask for, even if it means your paper gets rejected. Use your own scientific judgment. - Barb Bryant
Build on others' work. Quote them fairly and with respect. - Barb Bryant
Discuss your results in meetings and with colleagues before publishing. In bioinformatics, the risk of being scooped is minimal. The benefit of sharing and getting feedback is enormous. - Barb Bryant
bb, thanks for the comprehensive coverage! - Ruchira S. Datta
You're welcome! :-) - Barb Bryant from email
Thanks! - Mr. Gunn
A big thank you for the coverage bb - Yann Abraham
yes, just great, bb! - Claudia Koltzenburg