Jun
25

Entrepreneurship, Grants and all at BIO2014

Having just returned from a 1 day trip to San Diego for the BIO2014 meeting. I was honored to be part of the session called “Mining for gold – creating business opportunities from publicly funded collaborative research”. This session was organized by Dr. Kai Torbjoern Ingemansson (Principal Scientific Officer, European Commission). I gave a talk on “Using the CDD Vault for MM4TB”.

My fellow speakers also included Dr. Bonny Harbinger, (Deputy Director, Office of Technology Transfer, NIH) and Dr. Claire Skentelberry (Secretary General, European Biotechnology Network).

Hopefully we made the audience think more about how going after grants for small companies can be important to develop new products and drive collaborations to help change the way we do science.

 

 

Jun
19

Itching to get back in the lab

I thought I might never want to do this again, but a confluence of circumstances is making me want to do something. I am itching to get back in the lab. One day.

My last wet lab experiment was in 1998, sure I have managed others since then that did  experiments in my lab, or collaborated with others that did work I proposed. So it’s not like I have been away from the “lab” just kind of missing from it.

So much has happened in 16 years, automation, new dispensing methods, new methods, new tools. I am at that point where I really would like to test my computational hypotheses myself again. I did it in the past so why not go back to that.

Pretty frequently I have emails in the inbox from postdocs applying for a position in my non existent lab. It’s quite sad not to be at least be able to interview these people for my imaginary lab. Don’t get me wrong I am quite happy, if not ecstatic with my current collaborations, I just want a bit more freedom to test some ideas my self. For one I would like to contribute to help some of my friends with rare diseases in their families. I keep having ideas, but honestly I get tired with having to convince others to do the experiments when I could move quicker. I am an outsider and always will be, why should they listen to me?

So many things that I still want to do, perhaps a refrain that many of us have, but it keeps hitting home. It seems recently that I keep being reminded of the brevity of life itself.  Putting this all together, it also appears there is no time like the present to at least think about or consider what I want to do in the next phase of my scientific career. Though I probably would not want to go too far outside my comfort zone, a fresh challenge or change in direction might be just what I need.

My wish list: Find a treatment for Sanfilippo syndrome, Charcot-Marie Tooth and Giant axonal neuropathy. Work more on cancer, because it’s affected many people close to me and my efforts, research wise, amount to very little. I think  I could still maintain my interest in TB and other neglected diseases, but this work would remain with help from collaborators.

I will be at BIO in San Diego next Tuesday so if there is anyone there that can give me a lab I would be keen to chat!

Jun
11

Rare Occurrence Reception

Jill Wood from Jonah’s Just Begun has a cocktail event planned in New York next week to raise money to fund a postdoc in one of the labs doing Sanfilippo syndrome research. This is obviously something I am very close too.  It just shows the willingness and generosity of those involved to help out (Jonny Lee Miller and Kristine Johnson are co-hosts).

Jill also sent along a short video she and several other Sanfilippo parents made (with the help of Jill’s husband Jeremy!) and it has interviews with two scientists, Brian Bigger and Alexey Pshezhetsky as well as shows some of these beautiful children. Their future is very much in our hands to find treatments.

Please pass this along to anyone thats willing to support this cause.

Jun
10

A priceless opportunity to submit an article on rare diseases

It has been a while since I posted something of note and in that intervening period as it happens some “opportunities” were put in front of me. Many of these have consumed my time, e.g. writing a year end report for a grant, a new collaborative project which spawned a couple of manuscripts, and of course the usual manuscript resubmission cycles. Most of the time I decline new offers because there are not enough hours in the day. However I was approached by an open access publisher recently to see if I could organize an issue on rare diseases.

So it is my turn to throw the opportunity to you the audience. Do you have a manuscript you want to submit, a commentary, a protocol etc? In due course the journal will be announcing this initiative, but I figured I would give everyone a head start. yes its open -access, but there will be discounts for submission, which will be very reasonable etc.

I should add the journal is very new (1 year old) and comes from a highly respected group/ publisher.

You might ask well, what is my role, what do I get out of it? Well, I get the opportunity to write an editorial and submit it.  That’s it. I am not even on the editorial board of the journal so i have no say in what is accepted etc. No compensation either, perhaps if I can pull it off ultimately some thanks will filter down.

So why do it..well its complicated, but lets just say, I have published in one rare disease specific journal, and other rare disease related work has been published in general journals. I think if we are going to raise awareness of rare diseases we should get a good body of work together in a general journal that is open. Perhaps it could kick off a regular series of calls for rare disease articles, maybe even a whole new journal devoted to rare diseases??

So if you have any ideas or want to contribute just tweet me or email me – or better still comment.

 

May
19

Could the community contribute to an ACS Session for Jean-Claude Bradley?

Antony Williams and I were discussing last week ways to remember Jean-Claude Bradley. One way might be a session at the ACS in 2015, the 10th anniversary of starting his open notebook.

Who would be willing to give a talk on a topic related to open notebook science or any of the aspects that were close to Jean-Claude?

For example he worked on malaria research, solubility, melting points, publishing negative data, mobile apps, he used open-notebook Science, CDK, wiki, blogging, he self published, he created science games, he was into virtual reality..So there are plenty of topics there to cover or use as a starting point to expand. If you need inspiration watch a talk from last year at U of Delaware.

Who knows what might come from this but feel free to drop us a line- any or all help, ideas of people or topics would be greatly accepted. Why not do it totally openly, organize it openly, make it accessible to anyone (could the ACS even make the session totally open and free?)..hmm just a few ideas to get the ball rolling.

 

May
16

The Measure of the Man

It has been a truly awful week. A colleague, Jean-Claude Bradley passed away. I found out on Tuesday while traveling. I was stunned. We had met several times, enjoyed lunches in a pub across from his lab at Drexel a few years ago, chatted at Science Online in 2012 and on and on. I will never forget that he was one of the first authors I wanted to request a contribution from for a book we edited, and he and co-authors did it on condition it was freely available. Can you imagine trying to get Wiley to do it. But they did and this chapter was the first I have ever seen where every reference was a URL !

First question I asked myself was why have we lost yet another great person? Second question was why didn’t I just thank him for opening our eyes to open notebook science and just being totally open about science? For many it is probably about as radical as it gets, as the majority still hoard their data. I would say a handful of scientists have really truly made me rethink why I am doing science. Yes he and others made me open up more. I am not close to open notebook, but I am putting things on figshare, slideshare and trying more open journals. Perhaps a fitting way to remember Jean-Claude is to keep this going especially in chemistry  – push for more openess.

A great measure of the person is literally how invisible he was, yet he has affected so many that we are sharing our remembrances and the impact he had on us.

As I am a collector, here are some of these so far and I am sure this will grow as word spreads:

Chemconnector

Science 2.0

SteinBlog

Scientopia

Drexel

Chem-bla-ics

ScienceSeeker

TerraSigillata

On Twitter I started the hashtag #ThankChemists because I also realized without them I would literally not be here, I would be doing something totally different. I wished I could have thanked Jean-Claude personally.

 

 

May
07

Talks and poster for the next ACS meeting

I put a few abstracts left over from the last meeting in Texas into the ACS for the San Francisco meeting and so I will be busy in the coming months preparing for this.

see you in San Francisco, California, August 10-14, 2014.

PAPER ID: 22104
PAPER TITLE: “Collaborative Sharing of Molecules and Data in the Mobile Age”

DIVISION: COMP: Division of Computers in Chemistry
SESSION: Drug Discovery
PRESENTATION FORMAT: Oral

PAPER ID: 22120
PAPER TITLE: “Why There Needs to be Open Data for Ultra-Rare and Rare Disease Drug Discovery”

DIVISION: CINF: Division of Chemical Information
SESSION: Global Challenges in the Communication of Scientific Research
PRESENTATION FORMAT: Oral

PAPER ID: 22094
PAPER TITLE: “Expanding the Metabolite Mimic Approach To Identify Hits for Mycobacterium tuberculosis ”

DIVISION: COMP: Division of Computers in Chemistry
SESSION: Drug Discovery
PRESENTATION FORMAT: Oral

PAPER ID: 22091
PAPER TITLE: “Examples of How to Inspire the Next Generation to Pursue Computational Chemistry / Cheminformatics”

DIVISION: CINF: Division of Chemical Information
SESSION: Inspiring the Next Generation to Pursue Computational Chemistry and Cheminformatics

PRESENTATION FORMAT: Oral
PAPER ID: 22176
PAPER TITLE: “Applying computational models for transporters to predict toxicity”

DIVISION: TOXI: Division of Chemical Toxicology
SESSION: General Papers
PRESENTATION FORMAT: Oral

PAPER ID: 22186
PAPER TITLE: “New Target Prediction and Visualization Tools Incorporating Open Source Molecular Fingerprints For TB Mobile Version 2”

DIVISION: CINF: Division of Chemical Information
SESSION: Exploring the Application of New Technologies in Chemical Research and Education
PRESENTATION FORMAT: Oral

PAPER ID: 22183
PAPER TITLE: “Progress in computational toxicology”

DIVISION: TOXI: Division of Chemical Toxicology
SESSION: General Poster Session
PRESENTATION FORMAT: Poster

May
06

How open publications could help rare diseases – why it needs a shake up

Working with the Hereditary Neuropathy Foundation (HNF) on Charcot-Marie-Tooth and related diseases, we have started to put out quaterly updates to highlight research being funded and also fundraising efforts. The latest update covers some research using Zebrafish. This also set in motion a bit of thought a few weeks ago on open publications.
If you need to find out about what scientific research has been performed on a rare disease where do you go? Do you Google it? Do you try PubMed, do you even try Google Scholar, ResearchGate or one of the many ‘Facebook for scientist’ type sites. As a non-scientist, knowing where to look may be overwhelming in the vastness of the internet. As a scientist, navigating how to make your research more accessible is no less daunting for several reasons.

Vicious circle #1: firstly, if you are a scientist your first instinct is to try to publish in the journal that has the highest impact factor, this may then be reflected favorably on your CV, career prospects and potential for promotion.

Vicious circle #2: if this attempt at publication fails you edit the manuscript and try a lower impact journal, occasionally you may have a flash of inspiration and try a comparable journal or one in a different area so now your research may just get lost. Normally these scientific journals are closed access, which means that if anyone wants to read it they have to pay to read it or have a subscription to the journal.

Vicious circle #3: scientists get trapped in this ‘publish in journals that are free to publish in’ but then prevent others from viewing their work without paying money. I will be quite honest, as someone on the editorial boards of several journals from publishers like Springer and Elsevier, this lack of openness is hard to digest.

As a non-scientist the scientific publishing world may seem utterly perverse. On the one hand, in most cases your taxes funded this science and in fact continue to prolong this situation, on the other hand you ask should the science be freely accessible in order to spread the knowledge and findings? Not if you are a publisher. They would argue they have to make money and they add value to the publication process. Of course this whole ‘pay to view model’ presents problems if you are in need of lots of papers, because the cost quickly mounts up. Say you are a parent trying desperately to understand what science needs to be done to save your child or yourself suffering from a rare disease. A quick search of PubMed suggests 161,894 papers (at the time of writing this draft) that are retrieved with “rare disease” as a search term out of 23 million in the database at this time. For Charcot-Marie-Tooth there are over 3600 papers. Browsing through papers at random, one paper costs $39.95, another is $31, yet another charges $27 for 1 day access, some even charge less for shorter access. This is not like iTunes and you get pretty much any song you want for 99 cents. If papers were this price perhaps there would be less of an argument here. But that is not the case. Papers from NIH funded research are supposed to become freely available after a year of publication. This is a relatively recent change forced on publishers, which many still think did not go far enough. If you are a scientist, the added levels of effort required of submitting your own manuscripts through this system are just another thing to do, unless you pay the publishers to do this.

Increasingly we are seeing scientists paying to publish as open access, they basically shoulder the costs and make their article open online. This of course also depends on the journals and publishers. There are respectable publishers like PLOS, BioMedCentral (owned by Springer and publisher of Orphanet journal of rare diseases), F1000, PeerJ and 100’s more in which publishing a paper may cost from hundreds to several thousands of dollars depending predominantly on the Journal. There are of course also more predatory publishers that prey on the need for scientists to publish their work in order to get grants, but at the same time several vanity journals with low quality standards do nothing to raise the quality of science.

If you publish frequently as a scientist a significant amount of your budget needs to go towards making your science open access. There is also a growing number of scientists that will only publish in open access journals. These are however generally not the highest in terms of citation index, so a trade-off has to be made, openness vs journal impact factor.

The situation is very fluid compared to over 5 years ago when there were few publishing choices. Increasingly, there are journals in any given research area that will allow you to pay to open up your article. As a rare disease foundation, HNF encourages publication of open access science. We think this is essential if you the public are to be able to access the science and be aware of the latest developments. For instance the work we highlighted on the zebrafish was published in PLOSONE. In fact publishing in an open access journal brought this work to our attention in the first place. Waiting a year to get free access to NIH funded research should not be an option for anyone. Perhaps it’s time for someone like Apple or Amazon to rethink the science paper distribution model in the same way they have made music and books, respectively more accessible. People would pay $1 for a paper even for limited access. Its likely publishers would find other ways to make money or in fact, more people may download their papers at a much lower price. I have seen how access to free issues of journals for a month can certainly dramatically drive downloads.

If we are to increase the visibility of rare diseases, the scientific accomplishments of the 1000’s of scientists have to be accessible. There is room for many high quality open access journals for rare diseases and for that matter more general journals that encourage the publication of rare disease related science. We have seen from our own efforts to publish our ideas on CMT in F1000, an unusual, but a very supportive journal. Let us hope the future brings more openness for advances in CMT science.

May
02

Article visibility and open access : Making TB Mobile visible

Always it seems as scientists we are playing a fine line between being either “under the radar” presence and not over hyping our work and then also needing to be visible to collaborate, get grants and build our social reputation. A recent set of slides by Antony Williams highlights the importance of having an “online profile”.

I was reminded of this today as a little over a year ago we had a paper on TB Mobile published in Journal of Cheminformatics. I looked today and logged in at chemistry central and found that the paper had 4485 views and an altmetric score of 23. I am not sure really how useful this is, but maybe would have an idea of downloads. Highly accessed is one thing but what about downloads?

TB mobile 1

 

 

 

 

 

I dug deeper and saw that yes I had blogged about this paper and cited it. Nothing new there,

tb mobile 2

 

 

 

 

 

and dug deeper until I found how the paper compared to others in the journal. It came 13th overall in the journal and 2nd based on date. I think this is good. It would also be interesting if the ACS is going to do anything like this (or already has but I missed it).

TB MOBILE 3

 

 

 

 

 

 

In comparison to other open access journals how does it rate? Well F1000Research provides the number of downloads and accesses and social media shares. PLOS provides probably the most exhaustive metrics on articles I have seen with views, saves, downloads, cites etc.. what about the non open access journals? Are they under pressure to provide such high level metrics beyond most accessed or cited information? Probably not, but then do they really care. As authors we should care about how visible and how often our papers are downloaded. Funding agencies should care, our companies and institutions should care because, downloads and views equals visibility and publicity.

So back to the paper, it describes a free mobile app funded by an NIH grant to CDD, so views of the paper should translate to more people using it and if the reverse is also true, perhaps creating a virtuous circle. Ultimately driving more visibility of mobile apps for science and tuberculosis research was the aim. $1960 well spent in my humble opinion (or 50 cents a view).

May
01

1 year ago today..I published in PLOS ONE

Today marks the anniversary of my first paper in PLOS ONE with Joe Olechno and Antony Williams (Dispensing Processes Impact Apparent Biological Activity as Determined by Computational and Statistical Analyses). This was quite an event probably for all the wrong reasons in that the evolution of the paper was shaped by rejection after rejection elsewhere and then finally a disagreement on a press release. Getting this work out was about as tough as it can be. In the background a second unrelated paper at the same journal had a rocky time, and that’s putting it mildly. I have not given up on PLOS, but I am avoiding PLOS ONE for a while longer, I am happy to review for them and have done recently. The ‘dispensing paper’ as of today has 9205 views, it will be interesting to see how its cited.

Getting the paper published was followed by a brief wave of interest from blogs and a few journalists but besides a recent highlight in Nature Methods honestly thats about it. All efforts to get other screening groups or companies to do what we did on a bigger scale have basically been met with negative responses (with the odd exception). So is this burying heads in sand collectively something I expected? Well perhaps yes, when faced with something that makes you question the quality of the data you have been working with on such a huge scale, its probably human nature to say “well this is just something we already knew about but its ok, lets just dismiss it”. Unfortunately that’s probably not the best response. Issues with reproducibility of data aside, when its just plain wrong data, there are no two ways about it.

Honestly, I think if the paper had made it into Science there would have been a lot more calls to action, there would be some serious discussion on how we could just keep ignoring issues like this, maybe. Believe me its not sour grapes. Like it or not (and I do not wish to sound crass saying it) PLOS ONE just does not have the impact (or impact factor) of a Science, Nature or Cell. Then again neither do any of the other open access journals. We have to change this situation, we need an open access journal with a whopping impact factor to challenge the supremacy of Science, Nature and Cell. Will this happen soon, probably not unless we start citing PLOS ONE papers like crazy and perhaps at the same time they increase the threshold for acceptance and probably publish fewer papers. In my lifetime it might happen.

I am definitely committed to trying more open access journals, budgets permitting. Our recent foray into F1000Research was prompted by a freebie submission for rare diseases, and honestly the whole process was such a pleasure it renewed my faith in open access. I think this needs to happen more broadly. Open access may want to engage scientists more broadly, make it cheaper to publish but at the same time be stringent in what is accepted.

So what will I predict in a year on the dispensing paper, maybe there might be some follow up, maybe some additional data might be found to increase the scope of comparisons across dispensing techniques. Alternatively maybe it will just become a footnote, something referred to in a decade when another scientist makes the same observation independently and is rejected from publication in the highest impact journal, which just happens to be open access too.

 

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