Publishing & Collaborations, the good, the bad, the ugly

First up – hopefully the title grabbed your attention and I hope the content below reflects it. Second my blog reflects my real research life so to spare some people’s feelings some names will be omitted. Third these are solely my opinions and not those of any company I currently consult for, fourth full disclosure I am at the time of writing on the editorial board for Pharmaceutical Research (published by Springer and they pay a stipend), Drug Discovery Today (Elsevier), Journal of Pharmacological and Toxicological Methods (Elsevier) and Mutation Research-Reviews (Elsevier). Elsevier pays me nothing for the record.

I will be heading to San Francisco to talk at the Mol Med Tricon 2012 on Monday 20th in the following session SC8 Best Practices in Translational Informatics, (the fellow presenters are Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World, Joshua Snyder, Novartis Institutes for BioMedical Research, Sanjay Joshi, Solutions Architect, Life Sciences, Isilon Systems). I have posted my slides on slideshare and will be talking about the CDD TB collaborations. Putting this together got me thinking about what does and does not work in collaborations. So I am putting this out there. A week in my life.

As my previous blogs have covered collaborations I do not want to cover the same ground. The TB work has been a valuable learning experience. Firstly CDD was funded to work with lots of different groups doing TB research for a couple of years. In very general terms some took advantage of our cheminformatics and any insights we (I) could provide. So what I will present at the conference are some of the outcomes and ongoing work with many different collaborators, predominantly the really good ones. But honestly, now having worked in the space of TB for 3 years I can see why progress is so slow. Good collaborations are few and far between. You would think these researchers would be amenable to collaboration, well it is the exact opposite, it’s just as cut-throught as any other area and data hoarding is rife, even those groups funded extensively by BMGF and NIAID funds. I can see this because I have been involved in several different projects, and I and others are not happy with what we see. Example 1. Over 10,000 compounds screened by a multigroup collaboration vs TB 3 years ago, the data has been analyzed (I have contributed to this), no papers written up (although some of us have pushed), nothing published, no data released. Example 2. Several academic groups screening the same massive libraries of compounds and none of this data has to date been released, let alone the fact that they are screening the same compounds over and over again. Example 3. Collaboration with multiple groups finds FDA approved drugs for a TB target so far not exploited by anyone, 3 years on still working. Judge for yourself how I feel about seeing this. Example 3. is a particularly good example of how not to collaborate. So I will expand.

3 years ago – a group approaches us to develop a homology model for TB Target X and find compounds by docking into it. We get an expert in this area to build it at cost and modify it as needed. I then spend a good amount of time docking various libraries into target X, suggest interesting hits etc. By Nov 2010 we have at least one hit for target X which is an approved drug..Not long after funding to work with these group stops. So anthing done was on my own dime. From then on finding out whether any of the follow up compounds I selected were active has been strained. Here is my life – every few months sending an email ping abbreviated as follows. ” hi how are you, any news on the compounds, are we going to follow up, discuss etc – why don’t you try these compounds etc..” Once we had a phone conf. Once I saw some structures of compounds with data on a page. I made many I feel useful suggestions, compounds were sent to others to test. I find out things only when I email the biologist. Neither of the 2 parties are forthcoming with data. Hello, I found your hits people!! (I wanted to say that but I am a modest guy and the reality is without the homology model the contractor built, they would have zero to work on). Yesterday I do the usual bimonthly ping. I find out a compound I suggested last fall was also active. The group is waiting to discover the perfect drug. No sign of publishing anytime soon. Fortunately the world is a big place and there are other people out there that will work on Target X and they do not want to wait around while another 6 million people succumb to the disease. Treating any collaborator this way is a sure fire way to lose respect. Will I go the extra mile for these folks again..You can decide.

There needs to be a solution. BMGF, NIAID should absolutely set time limits on the people they fund to publically release data and publish what they have done- and ultimately SHARE their data. Yes of course data quality is an issue – but by hoarding the data the public does not get to see the lousy molecules people are testing. This I believe is called mandating data release..I think it is also the responsibility of any collaborator treated so badly that they should call people out to the funding agencies involved. That will certainly get their attention.

I am fortunate that 99.9%of collaborations are long and fruitful. An email out of the blue by a group to work on an interesting transporter during the week led me calling a longtime collaborator (10 years) to ask if I could borrow a model they had so I could work on the new project. Within an hr or so of the email a file appears. I call to thank them. I was in no rush for the file. But I am the same, a fellow scientist wants something, I listen and if I can help I get on it. My day is full of back and forth interactions with collaborations. I drew map last year of them all it was amazing. I will do what I can to help people because science for me is COLLABORATION.

Which brings me to the hot topic of publishing. Back in Aug last year I submitted 3 different collaborative papers in the space of a few days. Two went to one journal (which I am on the editorial board) and one went to another. Both journals are pretty well known, reasonable impact factor with great editors. Months passed by with no news or reviews. December and of course everything slows down so I enquire, no news. Janaury passed, and of course all my co authors on all 3 papers are wondering what is going on. I tell them multiple emails to the journals yielded nothing. Last friday I call both journals and email them with an ultimatum. They have 1 week to send me a response (after over 5 months in review) or I withdraw them and submit elsewhere. So the topics if you are interested were 1. TB drug discovery, 2. a nuclear receptor model and 3. a novel transporter model. The journal with one paper responds this week, deeply apologetic. Obviously the editorial board member tasked with review had “issues” or was obviously too busy to send my paper out for review or respond to my email. I address reviewers comments and resubmit (paper accepted minutes ago). I am still waiting on the two papers at the journal for which I am an editorial board member (2 hrs to go before I withdraw them).  They did however send me back comments on a paper I also sent  in December. I think Journals are overwhelmed. Its not me surely, 2 different journals, articles on different topics. The big publishers have issues dealing with day to day reviewing and editing.

So all of this connects in my mind with the discussions (shouting matches more like) of boycotts of certain publishers (Elsevier), AAAS  et al and people going open access. I listen to the arguments carefully. Am I swayed? What if I quit the editorial boards of these journals, is that really going to help? I review for them, should I stop? My answer to all of these is No. I publish in them because they are FREE to publish in compared to PLoS, BMC and other journals that will allow my article to be OPEN Access for $3000 a pop. Sorry folks I do not have $60,000 dollars to blow on papers this year! When I started writing scientific papers in the early 1990’s if people wanted to access your paper there was no open access, they just sent a postcard to the author and asked for a reprint ( I still have hundreds of stamps from all over the world because of this). Authors would send a nice shiny reprint or a photocopy in return. When I want a paper that I cannot get, I go to PubMed, find their email and ask the author for it. I can tell you that people in India, Cuba and South America email reprint requests to me all the time. Rarely do I get a snail mail request for a paper. I am responsive and ususally send the pdf immediately.

I think we have grown fat and lazy scientists in the US and Europe and we expect everything to be there for us. We used to send reprint requests but not any more – we expect that pdf at the end of a search in PubMed or Google. An email is easy. So they publish in Science, Elsevier, Springer etc journals. I am sure every author has their PDF of an article, it takes seconds to email them or get your postdocs to do it. So my solution is simple stop griping and boycotting and get on with science. I personally think is good for the publishers to have competition from PLoS  etc..I occasionally publish in them. But give me a journal anyday in which the quality and speed of the editorial / pages proofs is as good as a traditional publisher. I think the stuff big publishers do in bundling journals is pathetic and 90% of what they put out is of no interest to me. But the good they do far outweights the bad. Sure their business model should change but they are a business. If you do not want to publish with them and have money to burn fine. But do not tell other researchers what they should do. I am personally sick of the blogs and tweets and any I see I will retweet with “just ask for a reprint” added to it.

What I think we should push for is making papers on particular topics more readily accessible such as TB, malaria, neglected and rare diseases in general. This will cost publishers little but it may help to move these areas along. But I think there is a more fundamental need that is missing here. Scientists need publishers (whether closed or open) and vice versa. Scientists also need other scientists and I think its time some of them took a course in collaboration 101 perhaps funded by BMGF or NIH.



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  1. Ross Mounce says:

    you may also be interested to read this:

    of Open Access journals that charge an Article Processing Fee – the average cost is just $906 – a price definitely worth paying to ensure that EVERYONE can read your work. http://www.openaccesspublishing.org/apc2/

  2. sean says:

    Many thanks Ross. Unfortunately for all the journals I publish in the cost is $2000-3000 a time. For example the Springer Journal Pharmaceutical Research wanted $3000 this week for a perspective. This going rate is generally the norm I have not seen anything lower. Occasionally we split the costs between authors but these are the exceptions rather than the norm. I think my personal upper limit would be 100-200 dollars per paper! Even at this level with the number of papers I publish this would amount to thousands per year which way outside my budget. As I said in the blog, everyone can read my work if they want – just send me an email reprint request, I am more than happy to send a pdf. One thing I have noticed is some publishers are so tight they do not even send authors a copy of their final pdf which is pathetic and that has to change (I would say a good example here was Bentham).

  3. Alex Clark says:

    I was under the impression that sending people PDFs of a paper was a violation of copyright, except that the journals turn a blind eye to it because they know that their business model doesn’t stand up to serious scrutiny. I don’t remember anyone ever actually telling me that, but I just assumed it was analogous to ripping a CD and sending it to a friend. So with this in mind, it seems like emailing and author and asking for a digital reprint is asking them to break the law in order to save you some money. That could be why it doesn’t happen more often :-/

  1. Disruptive Strategies for Removing Drug Discovery Bottlenecks – My experiences of a closed access publisher » Collaborative Chemistry says:

    […] with Science certainly was not encouraging anyway, lets see what this more open approach brings. Based on my recent experiences of peer review at other Journals including Pharmaceutical Research an…I am becoming more convinced that this model is sustainable. I think it too is undergoing a […]

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