This is the third and final post in a series in which I
share some lessons learned about how to plan, manage, analyse and deliver a
‘big biodata’ project successfully.
Now that you have the results of your carefully planned,
meticulously managed and diligently analysed experiment, it’s time to decide on
what to publish, and where.
1. Present your work
I love presenting, because having to explain my work to a
mixed audience helps me understand and articulate the science better, and to convey
the excitement of discovery. What is the work for, it not the joy of
exploration? Creating figures to use in a presentation is enjoyable, and helps
me get my thoughts in order.
I find writing paper less enjoyable than presentations, but
the same core is present in both – good figures which provide a strong narrative from design through to analysis. There is however a particular
rigour in writing a paper that brings out the best in a piece of scientific
work. Present, and publish – it’s important to us all.
2. Organise your material
Most of these papers comprise both a main paper and a
supplement. The main paper will feature the figures that tell the story:
experimental design, discovery, main findings, interesting cases. It should be
written for the interested reader who will mainly trust you on the experimental and
analysis details.The supplement is for the reader (including a reviewer or
two) who does not trust you. Sometimes, on other people's papers, you will be that reader. The
supplement should have the same flow, but have all the supporting details that
tell that reader the data and analysis are kosher.
3. Figures first
Make good figures that illustrate your point, and test them
out in presentations, first to the group, then to colleagues in your institute,
and then more widely. You’ll fine-tune the figures as you go. Your presentation
will need quite a bit scaffolding (why the question is interesting, about your
experimental design, key statistics), but don’t be afraid to show sample data from
your results to show your motivation. Consider showing a boring and interesting
case side by side. You may find this scaffolding can be condensed into your
Figure 1 for the paper. You can show other figures in the supplement if they
support your work.
4. Put pen to paper
Once your figures flow, you can write the results. You can
also start working on the supplement, following the same general flow. All the ‘data
is good’ plots will go in the supplement, as it can have extra “lemmas” about
the data. Don’t skimp in the supplement – include technical details supporting
things like, why your normalisation is sensible, or better than other approaches.
If the supplement gets big, provide an index on the supplement for navigation. The
sceptical reader will like to see this.
5. Focus on the results
Write the introduction and discussion after you are happy with your results write-up. Think about the
readers and the reviewers, and make sure to cite widely. If you are coming into
a new arena with this high-throughput approach, lavish praise on the importance
of the field and the massive amount of individual loci work on which you are
building. Basically, if you are publishing a large-scale approach in an area
that hasn’t had one, avoid being seen as an interloper; read the papers, cite
them – and you are likely to find a couple of new angles on your work through
this process.
6. Length angst
If you are aiming for a journal with strict length limits (and I do wonder why we tolerate this in this day and age), don’t let that hold you
back at the submission phase. Write as much as you need to, and acknowledge the
length in your cover letter. Emphasise that you want the reviewers to have a
full understanding of the science. For these more restricted space papers,
reviewing at that density is often really hard – the text can be edited after review.
7. Be open
It is pretty standard that you will be publishing eventually open access (certainly if you are NIH, or Wellcome Trust and other funders). It is easier to do this via journals which automatically handle the open access submission (Plos, Genome Biology, BMC series and many others, sometime with open access fees). Due to the funder mandates pretty much every journal will at least allow submission of your author manuscript to PubMedCentral, but doing it yourself is quite annoying.
There are new experiments in open publishing as well to look at. Two examples are F1000 and Bioarxiv. In F1000 the whole process of submission, peer review and publication is done in the open - it interesting to watch open peer review in action. Bioarxiv is following the more physics pre-print server, and many journals allow pre-print posting whilst a paper is under review. This is a cool way to stop being scooped and provides a way to get community input ("informal peer review"). I think we're in an experimentation phase of this next stage in open science, and it's going to be interesting to see where we end up.
8. Tidy up and submit your data
Make sure you have all the raw data to submit, with the
meta-data nicely tidied up (ideally, your LIMS system will have this ready to go
by default). Submit your structured data (DNA, Proteomics, Metabolomics, X-ray structure, EM) to the appropriate archive (EMBL-EBI has the full range). Have a directory that you keep in house; otherwise, put all the
intermediate datasets and files on the web. This is good for transparency – the sceptical reader will be even more reassured when he or she knows that they can (if they want) not only get the raw data (a given for molecular biology) but can also come into the analysis half-way through. About half of these readers could be future members of a group you may ask to
"follow the analysis in paper A", or to confirm that "XXX did this in paper B". Do this for your own group's sanity and for extra brownie points from readers around the world.
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