Chris Miller › Likes

Cyndy Parr tweets ( http://twitter.com/cydparr... ) "This is kind of what PLOS One envisions -- it goes up there, and then it could get chosen to be part of a hub". Iz true? - Karen James

Thanks, Graham. Having just had a paper rejected by two journals in a row, I'm fed up to here *points to own eyebrows* with spending hours if not days re-formatting to meet the ridiculously precise but in no way substantive guidelines of different journals. It's not even rewriting, it's just pointless fiddling and a silly waste of time. If the taxpayers only knew... - Karen James

There are two issues at hand here. One, a universal format for submission, Two, a bidding process on papers. The Neuroscience Peer Review Consortium points to how the second part of this kind of deal is working right now in some disciplines (http://nprc.incf.org/), the really really sad part about the first issue here is that the big publishers don't care what format you submit in (let... more... - Ian Mulvany

+1 for more standards for paper submissions, starting with reference styles. And for allowing submissions in the NLM DTD format. - Martin Fenner

Ian, you may say they don't care, but when one is submitting a manuscript, one is trying to do everything one can not to give the publisher any possible little excuse to reject your paper without review. - Karen James

Second time in a week that someone stated "publishers don't care about format of submissions". Again I ask: if that's the case, why do all journals make a huge deal about it in their instructions to authors? - Neil Saunders

As for universal format: easily solved by writing our papers on the web. Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... Imagine a button in Google Docs that says "submit this document to <insert journal here>" !! But currently, we all like to use our own word-processing software on our own machines, then upload a document in a multitude of formats. It's going to take a big shift in thinking and work practices. - Neil Saunders

What Neil said: if journals don't care, why do they make such a damn song and dance about it? Why not explicitly say you can *submit* in any basic AIMRAD format? Worry about format after acceptance: either the journal can send it to India per Ian above, or if they make the authors do it at least they only have to do it once. My next paper (quit laughing) is going out in basic AIMRAD... more... - Bill Hooker

Note: this is easier for me to do than many, because I've basically given up on an academic career as currently constructed. - Bill Hooker

"it's just pointless fiddling and a silly waste of time. If the taxpayers only knew" I think they should / deserve to know! - Björn Brembs

+1 Neil "why do all journals make a huge deal about it in their instructions to authors?" and +1 Björn "I think [the taxpayers] should / deserve to know!" - Karen James

Neil & Bill: maybe "don't care" is to strong a phrase. A manuscript does need to be structured correctly to fit into the journal's content management system (an application note looks different to a letter looks different to a research paper), have images properly resized and references in the right format so that they can be processed by systems that convert to them links etc. - Euan

Also: what happened to that Wolfram word processor for papers that was supposed to do what Neil mentioned above with Google Docs? - Euan

Ah, http://www.wolfram.com/product... but doesn't look like there's a great deal of support for life sci journals (BMC aside) - Euan

the publishers i know would be delighted to standardise to NLM DTD for submissions -- would save lots of editorial time and production costs -- the publisher i know best sends accepted papers to be manually turned into xml which can then be used for PMC deposition and the semi-automatic generation of the HTML and PDF versions. But things like the Publicon app have taught publishers that implementing the technology to do something doesn't mean that it will happen in significant quantities! :) - Joe Dunckley

I used Publicon when it was released a few years ago. Essentially a dead product now. Lemon8-XML does what Neil describes as "Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... ": http://network.nature.com/people.... - Martin Fenner

These interviews (about eXtyles and Editorial Manager) might be interesting to those that care about submitting papers in the NLM DTD format, as I specifically asked that question: http://network.nature.com/people... and http://network.nature.com/people... - Martin Fenner

There is a nascent version of that working in neuroscience http://nprc.incf.org/. Journals have formed a consortium where if an author submits to one journal and it gets rejected, the author can specify that the reviews follow the paper to another journal so that it doesn't need to be re-reviewed. This was viewed as a way for papers that have nothing wrong with them but which don't fit the scope of the journal can be published more quickly and easily. - Maryann Martone

What about replacing "papers" and "journals" in the subject line with "proposals" and funders? - Daniel Mietchen

What if journals said here's our LaTeX template. Put the right text in the indicated field, lotion in the basket, and anything else won't be accepted. - Mr. Gunn

@Daniel Mietchen: Yes, that too! @Mr. Gunn: What I'm advocating is that there's a single LaTeX (or whatever) template - not that you'd re-paste for each journal. - Karen James

karen, yes. The idea being you give them the text and they do whatever they like with the formatting. - Mr. Gunn

Aside from making life easier for authors, it would allow sane computational use of papers. With PDF, you don't even know which image a figure legend refers to, except by guess work. The difficulty is that the journals don't see it as their problem. The solution is for the authors to make it the journals problem - Phil Lord

I like the idea, Karen. Publishing an exciting paper should not a be a torture (for us!) - Betül

Getting access to research papers is already too expensive. Wouldn't it just be more so if we invited a bidding war on each paper? Write good papers, and submit them to PLoS. - Ted Slater

Ian York rocks, as do the scientists who did this. - Mr. Gunn

Gels still speak, even without lasers... - Mark A Jensen

should be on the desk of anybody doing machine learning - Rajarshi Guha

Wonder how they got Springer to agree to this?! - Noel O'Boyle

@Noel: I guess because the understand not everyone has a kindle yet? :) - Egon Willighagen

Bosco, this is a superb idea. Along with starting up a new journal/software hybrid, it will be great if existing journals insist users to submit source code, executable or VM of a bioinformatics software / database / server to a centralized repository like 'biohub.org'. - Khader Shameer

This is a good idea. - Michael Barton

While not linked to an actual repository (but rather, provides a snapshot of the s/w and data for the article), Journal of Statistical Software, does pretty much this - Rajarshi Guha

I would take this further and the article text remains in the revision repo. The reviewers are sent to the article, not the other way around and it can be forked in just the same way the software can - Frank from iPhone

@Frank, this makes sense, since otherwise the paper would be static and refer to old versions. But then this assumes that as the s/w is updated, so is the paper - Rajarshi Guha

@Rajarshi not neccessarily the paper should state which version/revision it refers to. It does not have to keep up with the sw. That is what documentation is for :) - Frank from iPhone

me likey too - Deepak Singh

The more I think about it, the more I think some big-wig bioinformaticians should do a deal with Google Code to edit a journal. That might even align with Google Scholar. - Bosco Ho

@Frank, in that case, why bother with a VCS? Why not just put a tarball with the source code for the version that goes with the paper? - Rajarshi Guha

Great idea, but I can't see it working for data sets. Yes data sets evolve and should track provenance somehow, but having been in and around standards groups for some time now, this is an impossible task for a publishing group to take care of, especially considering the nature of big-data bioinformatics. Plus if goes against best practices for software source control (use factories, don't store your database...) - delagoya

There are some interesting and non-trivial questions around this kind of idea as to what peer review should look like. Should such a journal provide virtualisation environments so that the code can be run? Example data should be a requirement presumably? Are peer reviewers expected to evaluate code "quality". Anyone thoughts on this would be extremely useful...and help guide a project like this into reality. - Cameron Neylon

My answers to Cameron's points: (1) no, (2) yes, sample data would probably be used to run tests which should pass, (3) quality is somewhat subjective - minimum requirement should be that code runs and generates output as expected - but reviewers could certainly suggest code improvement where appropriate. - Neil Saunders

So if the answer to 1) is no, does that mean that you can't necessarily expect referees to actually run the code? Or compile it? Or just that you pick referees appropriately? Or conversely that "refereeing" becomes a process of building up enough positive comments or karma points in the repository...? It seems to me that you want to bring the best of versioning systems and best practice... more... - Cameron Neylon

Referees should certainly be able to run code - I'm just not sure that virtualisation through the web interface is the way to do it. Seems like an additional layer of complexity that might get in the way of making this idea work. - Neil Saunders

@Cameron & Neil: If it could be figured out how to to handle the virtualization (or having remote access to machines), I think that'd be a highly valuable addition to peer review. Easy for me to say (not knowing how to implement it), but I think it's a great goal to strive for. It doesn't seem too crazy to have the journal have a bunch of machines on hand so the authors can remotely upload / install code and referees could then remotely log in to look at and try out code. - Steve Koch

I can't figure out where to jump into this thread. Personally, I think we just need a place to publish locations, i.e. the code is here, data is there and this is the version we used, etc. That must be maintained and being able to maintain that should become part of the funding process. Since funding agencies are the ones who are funding this research they need to include the ability to... more... - Deepak Singh

My feeling is that being able to run the programs somewhere on a server without downloading them is important - but that is very much a user's perspective. I often look at useful things that are made available and just have no clue how to actually make them work. A good range of downloadable executables would probably do the job for me though. Additional question: what are the standards for web services? - Cameron Neylon

Which is why VM's and cloud services are such a big deal for demo's and provenance now. You can package up a VM with the exact stack that you want and make it available, either as a service or a VM you can launch yourself. It's too easy not to do it - Deepak Singh

@Deepak : Cloud + VM is an an interesting combination, but should have an accessible pricing that is affordable to a larger research community - Khader Shameer

I think there should be strict guidelines while reviewing bioinformatics software / database / servers to test the resource. I had a recent experience : a reviewer wrote extensive list of points to reject a server that we developed with out trying what exactly it is doing or to know how does it differs from other existing resources. I strongly support the hybrid journal model, also it... more... - Khader Shameer

Let's talk specifics. VM images are great, but you are tying your release to a particular release of a particular platform. A better approach is to start from a base OS (like a linus distro ISO) and have a set of build instructions for system set up and application building. My favorite of the moment would be Chef. - delagoya

Second, academics love to solve a problem with a novel algorithm and then move on. In fact it is in their best interest to move on after milking a project for all it's worth, publication wise. Maintenance, or even robust testing (couch... Tophat ... cough ... Bowtie .. cough ) is not even on the radar. Frankly I am not so sure it should be. Maintenance requirements may slow the pace of... more... - delagoya

@delagoya, good point. If I have made significant improvements, why update the old paper? better to try for a new paper! - Rajarshi Guha

delagoya, chef's fine too. Find a common medium/mechanism that works for the community. The resources are certainly there. It's a matter of trying things out. As someone I know says, start simple, and iterate - Deepak Singh

Khader, that's where the funding agencies come in. They need to provide mechanisms for sustainable funding here. - Deepak Singh

The nice thing about a hybrid journal is that it might be possible to have new dois/database entries for "significant" updates. Not perhaps just place holding papers as is the case sometimes in the NAR database issue but when something has changed significantly you can get a new paper without needing a new algorithm or service. I like the idea of funding to support "orphan" code and services as well. Make it worth money and people will do it. - Cameron Neylon

Delagoya - as a naive user I disagree. I really don't want to have to build, I want to use in the lowest stress way possible and a hosted VM seems like a good way to enable that - as well as allow for longer term preservation. We may not be able to run linux on future hardware but will probably be able to handle VMs for longer (actually having written that I'm not sure its true - would be interested in more expert perspectives) - Cameron Neylon

I almost missed this discussion. I really like the idea but I wonder how discovery type projects fit in. I mostly use code to look for trends. If anything I might make some predictor to enhance existing data. For these reasons most of what I do is one off scripts around perl and R. Maybe this sort of project does not belong in a bioinformatics journal at all. - Pedro Beltrao

Pedro, great question. Personally, if we included all glue code, small scripts, etc this would be unsustainable and defeat the purpose of peer review as well - Deepak Singh

@Pedro, I don't see a journal/software hybrid as replacing all bioinformatics journals. I think there's a place for journals that discuss pure algorithms and ideas. These would do exploratory type programming. Normal journals service these papers quite well. For me, a hybrid model targets specifically those papers that describe a program that is meant to be used by other people. In that... more... - Bosco Ho

Bosco, you're thinking along the lines of a communications journal aren't you. And then people can go to work on the code if it is on github or something - Deepak Singh

@Deepak. Yep. The disconnect I see is that pragmatically, it's the open-source project that counts. The article in the bioinformatics journal is so that we can get a place-holder to collect citations that contribute to our academic CV. The journal/software hybrid provides the most efficient way to this goal. - Bosco Ho

Me too, re: Google Wave gadget. Then add SBML support, use SBGN in the display, support MIRIAM annotations and I can retire penniless. - Neil Swainston

@Neil, there are a few other tools which support SBML and SBGN (see http://sbgn.org/Communi...). Wikipathways seem to be inventing yet another pathway format and dont provide a conversion to any other existing "standard". Shame as it would benefit everyone if they did. - Frank

Thinking about it a little more, I'd really like to see the above refactored as a collaborative Google Wave Gadget. I've been involved in about five network reconstruction "jamborees" now, which involve flying loads of people around the World to sit in a room and discuss things that they could do with PathVisio (if it supported SBML...) or Payao. Anyways, this costs a fortune (see the... more... - Neil Swainston

You can query ncbi:eutils/elink e.g. http://eutils.ncbi.nlm.nih.gov/entrez... but, as said, Andrew, the database is not fully complete. - Pierre Lindenbaum

www.novoseek.com/, www.nextbio.com, biosemantics.org/geneE/search.jsf, and www.ihop-net.org are some resources... - Jeff Kiefer

Thanks for the pointers, useful to start with - Rajarshi Guha

The trick is not to start with a PubMed search for the gene name, but to start with the NCBI Gene database. All of the Entrez databases are linked so you can go from a Gene record to publications. Use either EUtils as Pierre and Andrew said, or go from the Gene page (e.g. http://www.ncbi.nlm.nih.gov/gene...) and follow the links. - Neil Saunders

geneRIFs might not be complete, but how complete do you need to be? - Mr. Gunn

@Mr Gunn, my application doesn't really need authoritative information. Basically, I'm trying to get a rough idea of which genes are more popular than others in terms of publications. Given that a pub may mention a number of genes in passing, it's not a very reliable measure. But it's one other feature that I can use in a summary/ranking etc - Rajarshi Guha

Rajarshi, it sounds similar to an analysis that we did previously to create what John Hogenesch calls the "sexy gene list". See http://www.ncbi.nlm.nih.gov/pubmed... and Figure 1 of http://www.ncbi.nlm.nih.gov/pubmed.... We used gene2pubmed (ftp://ftp.ncbi.nih.gov/gene/DATA/) and an awk/sort/uniq one-liner ... - Andrew Su