Aug
25

PLOS paper going viral?

There is just too much going on now with the whole Ebola virus outbreak and the ALS Ice bucket challenge to really use the word “viral”, but I will use it regardless. Last Thursday at 2pm a small editorial co-authored with Ethan Perlstein went live at PLOS Computational Biology about ten simple rules for live tweeting at scientific conferences. The response has been pretty amazing, I think its as close to viral as anything I have ever been a part of.

I happened to be on a 2 day vacation to recover from the previous weeks travel at the ACS, but instead devoted half a day to posting an article on this blog, tweeting and thanking the retweeters “live”. It sounds absolutely ‘nutty’ as I write this. I am a relatively sober scientist, but over the past year I have begun to follow how blog posts and twitter can have an impact on reaching potential readers of scientific articles in open access journals in particular. I am using open access journals because in most cases it is pretty easy to follow the metrics, like views, shares, downloads etc. PLOS are pretty handy like this. Some open access journals make the information only available to authors, but not PLOS, F1000research etc..

Last year we had a paper on Acoustic dispensing and computational modeling in PLOSONE that achieved considerable views primarily because of a blog post from Derek Lowe which stoked interest. To date in over a year it has over 10,300 views, 6 citations, 47 saves, 122 shares etc, not bad going in 16 months. But I am still having a hard time seeing if it will have any lasting impact, does it make a difference?

Then comes the latest editorial / paper and in just a few days it has over 7300 views and over 660 shares and this is growing by the hour. Why? Both Ethan and myself tweeted out the link and had considerable retweets. I tweeted each rule and that had no effect. So I think what has happened is that Ethan’s well connected network of 4707 followers has really made its impact felt and they have in turn retweeted it and so on. For instance PLOS Computational  Biology retweeted to their > 4000 followers. We have helped, personally I have thanked many of the retweeters and inturn I have seen that this act alone converts many into new followers. Whether this continues is another matter. Its time consuming but this is a kind of experiment in seeing if using Twitter can actively help promote an article about using Twitter. A nice circle.

So I was wondering what this means too if anything and how do we measure impact?

First we picked a topic for a “Simple Rules” editorial that has hit a nerve in a really good way. While the journal is a computational biology journal it clearly does not seem to put off people coming to it to see the article. Perhaps we would have the same impact in PLOS ONE? While the article is not in anyway about computational biology it is relevant because of the use of sharing scientific insights etc using computational methods – namely live tweeting. Not sure this is really justification. But on another level if we are to communicate science whether its ecology, evolutionary biology of computational chemistry or biology we have to do this optimally. At this point in time Twitter is a way to communicate that has created a pretty good sized user base with 271 M monthly active users. If we can get other scientists to communicate in turn what other scientists are saying and seeing at scientific conferences we could have a massive magnifying effect. Sure some of it will be meaningless but we will get information out there and anyone searching for scientific topics will find it. A great analogy here is perhaps ‘scientific scrapbooking’. We piece together all the small tweets into some coherent whole, or software will make sense of what is coming out of the patchwork of data. We are part way there with ODDT being able to collect tweets on a disease or topic and being chemistry aware. What would an app or software need to have to be truly universally science aware (that is handling structures, images, molecules, all kinds of data etc).

I have asked if new scientific conference live tweeters will let me know when they do it. I am not expecting them to remember. So what can we do to keep the memory of the article fresh? Well As people suggest new rules I am adding them to the article comments. Sure this list may grow, but a bit of audience participation might be a good thing. It would be great if some journalists or a blog picked it up and spread the word but I am not proactively doing this. We have had questions on Twitter about the ethics of sharing hashtags for conferences before they start, some people thought our rules a bit obvious so I think keeping the discussion going and perhaps engaging some conference organizers would be smart. If major conferences had scientists actually live tweeting and perhaps even professional live tweeters (..now there is a new job for the resume) that would certainly raise the visibility. For example the ACS occasionally has individuals tweeting out new molecules as they are presented. But what if BIO had people tweeting live and SLAS, and Neuroscience (insert your favorite science conference here).

Now back to doing science and occasionally Tweeting about it.

 

Aug
21

Anatomy of a PLOS Computational Biology Paper

I think the following is a fair representation of what kicked off the very short editorial paper published today in PLOS Computational Biology. In addition the timeline gives an idea that coming up with the manuscript was quick relative to publication but isn’t that always how it is, the idea is easy relative to getting it published.

1. Feb 11-13 attended Lysosomal Disease Network 10th Annual World symposium in San Diego – I was live tweeting from talks and posters as well as presenting a poster on ODDT and rare diseases. Walking to dinner one night with Ethan Perlstein we discussed the lack of live tweeters and the 1000′s of patients globally that could benefit from hearing what was going on a the meeting. We discussed the idea to write a paper on how to live tweet at such scientific conferences.

2. Feb 12-13 we send a couple of draft emails to each other called “10 simple (10 commandments) rules of tweeting at scientific conferences”  and also do a literature search for other guidelines on tweeting.

3. March 3rd we had a final draft paper and it was submitted to PLOS Computational Biology.

4. March 4th – I had to change article type to an editorial and update financial disclosure.

5. April 10th – first automated email telling me paper was in review.

6. April 30th  – reviews received

7. May 11th – Corrections submitted

8. May 22nd – June 17 multiple communications with Editor and PLOS staff to find out if paper is now acceptable.

9. June 18th – paper acecpted

10. June 26- July 14-  Had to work on a new image as we submitted one of a phone displaying twitter logo, a room packed full of attendees at a conference and a picture of the world..needed to be CC BY 4.0.. At this point I engaged my cousin Neil Dufton who has a talent for illustration.. However we also benefited greatly from assistance at the journal to increase resolution which always seems to be an issue with the figures I submit here. Image resolution is not my strong point.

11. July 24th Copy edited manuscript edited.

12. August 21st – published.

Our goal with this is to reach people who have never tweeted at a conference before and maybe this will serve as an entry to live tweeting.

If there are other useful conference tweeting resources we missed please let us know and I will post on the PLOS comments page.

We hope this will represent a basic primer for tweeting at science conferences. It is easy, it is fun and you get to know people all over the world that appreciate your sharing what you heard and putting it in a tweet.

 

 

 

 

 

Aug
18

Rare diseases collection at F1000Research

I have mentioned previously that I have the honor to edit a collection of articles for F1000Research. So here is your chance if you are in the rare disease community and you have something you want to publish..do it now! Having published previously in F1000Research with collaborators I found the process was simple compared to other open access journals. The editorial feedback on the article was excellent and the team behind the journal are very responsive. So if you have any traditional research articles (including clinical trials), as well as reviews, data notes, observation articles, case studies, method articles, and software tools (for details see the author guidelines) on rare diseases please submit them.

I am looking forward to seeing if we can make this into something more than a rare disease collection but maybe something more regular which highlights rare disease research in an open and accessible fashion. As I have said before, I think open publications could transform rare disease research.

Aug
15

Déjà vu – Another family affected by a rare disease trying to find a cure

During my trip to San Francisco this week I had the opportunity and honor to meet with Matt Wilsey, one of the parents of a child (Grace) with a rare disease and the President of the Grace Wilsey Foundation. The diagnosis of Grace’s NGLY1 deficiency was recently highlighted in an excellent article in the New Yorker by Seth Mnookin. The article also touches lightly on some of the issues with collaboration, competition between groups and publication. Matt and another parent of an NGLY1 child Matthew Might, published a commentary in January on clinical diagnostics and next generation sequencing. In all of this it is important to note that without these parents pushing there would be no understanding of NGLY1, all the scientific progress is due to them fund raising, funding research and their persistence.

So I met up with Matt in a coffee shop across from the Powell St. BART stop for about 40 minutes. The day before I had given a talk at the ACS meeeting to a small group on why there needs to be open data for rare and neglected diseases. What do I know? This is where it gets fuzzy as on one hand I am a scientist trying to piece together the fragments of biology and chemistry and find connections that might be useful. On the other I have now become a defacto rare disease advocate and champion. I sit in an uneasy position. Its not something I can take lightly. Chatting with Matt half hidden behind the largest bottle of water imaginable, I had a déjà vu moment, seeing the same phenotype time and time again with some rare disease patients/parents. Their optimism, knowledge of everything and everyone associated with the disease is worn front and center. That is in itself a superpower that can open doors. They can say and do things regular scientists could not. They can doorstep high ranking officials at the NIH, FDA, congress and they can get time with the busiest Nobel prizewinners and CEO’s. These rare disease parents have an unwillingness to just accept the disease diagnosis, but to meet whoever it takes that can unearth a piece of the pathway to the cure. This pathway may be long, as Matt presented me with a heavy business card listing the NGLY1 3 line long phenotype. All of these rare and ultra rare diseases are frightening in what they do to the patients and families.

As I am sat there listening, I was mesmerized by the fact that this disease shared some similarities and symptoms to some of the other rare diseases I am acquainted with..Its an enzyme that cleaves sugars on proteins, its symptoms include peripheral neuropathy and there may be proteasomal involvement. After the meeting I introduced Matt to some of the parent advocates who have taken a similar pathway to Matt for their diseases. While Matt is literally at the beginning I also sense that he and others can go faster if they can learn what works / does not work.

So this goes full circle to my talk on needing open data. If scientists could freely share their data and reagents faster progress would be made and any unnecessary repetition could be avoided. How do we catalyze this? I sense this could be very important because what may be learnt from another rare disease might help NGLY1. Conversely data from this disease may help others.

Later that day I am sat at the ACS in a room packed wall to wall with hundreds of medicinal chemists listening to some of the most senior medicinal chemists at the biggest pharmaceutical companies in the USA. The diseases they mentioned were dominated by cancers, the targets predominantly kinases  and in general there was not a heavy emphasis or barely a mention of rare diseases.  There was some occasional mention of collaboration but nothing obviously on openess. So here we are with a great opportunity, put chemists to work trying to develop chaperones for diseases like NGLY1, or thinking of ways to get enzyme replacement therapies that could target where they need to go to work in humans. Sitting there hearing that more and more medicinal chemistry expertize is leaving our shores for China did not fill me with hope, but it did get me wondering what if we could convert a few big pharma chemists to the rare disease cause.

I was kindly introduced to Matt by Ethan Perlstein who himself is doing his bit to help rare disease research including NGLY1. Curing 7000 rare diseases may take a few good medicinal chemists and champions that can make things happen, parents like Matt would be eternally grateful.

 

Aug
14

A poster and 3 more ACS talks

Tuesday and Wednesday at the ACS were pretty full up with meetings, talks and posters.

Tuesday I gave a poster entitled Progress in computational toxicology – which generally shows a pretty good agreement between different machine learning methods and various toxicity datasets. It also served to highlight a new tool we have developed with Alex Clark and Krishna Dole called CDD Models. This is a beta version of an open source Naive Bayes method with open source FCFP_6 fingerprints, so you can now build models in your secure CDD Vault. This work was funded by an NIH NCATS SBIR and we still have a way to go – ultimate goal to enable sharing of models if desired so they can be made open source to if desired..

First up on wednesday was a provocative talk on “Examples of how to inspire the next generation to pursue computational chemistry / cheminformatics“.  This talk was inspired over a year ago about thinking how to encourage children to interact with molecules after watching them play with perioidic table apps that show videos of the elements.

The second talk was “applying computational models for transporters to predict toxicity“.  This highlighted about 5 years of work in a 20 min talk – all achieved through collaborations with experimental groups.

The final talk “New Target prediction and visualization Tools incorporating Open source molecular fingerprints for TB Mobile version 2” was a summary of the recently published work from Alex Clark, Malabika Sarker and myself. The app now has a heavy dose of cheminformatics (bayesian models, clustering etc.) and is pushing the boundaries for a chemistry app that combined cheminformatiocs and bioinformatics information as well.

Well until Boston in 2015..lets see what I will have to present for that one.

 

 

 

Aug
11

ACS in San Francisco..6 talks and a poster

For a few days I am in SF presenting several talks ..In all but one case I plan to post the talks..

Yesterday’s talk was on collaborations. The prior speaker did not turn up so I gave it twice.

Today I gave two presentations. One on TB mimics. This work is subject to some papers that need to be submitted and so It may be a while before the slides are made available.

The second talk was on the need for open data for rare and neglected diseases.

Over the next 2 days I have a poster and 3 more talks to go.

Putting these talks together is a challenge because you just never know who is in the audience. It’s also quite important to give new fresh presentations and discuss some topics that may be a bit provocative.

Obviously the link between all the talks is really collaboration of different flavors. Whether that is large scale, small scale, closed, semi open or fully open. The ACS also ensures pretty much that there will be some interesting discussions which really is probably just as important for someone like me that works from a home office most of the time. Getting out and engaging the audience is important.

One thing I took away today from a talk by Amy Beisel (Research Square)  is the importance of reaching out to non English speaking authors as a journal editor or reviewer and try to be more sympathetic to the fact that their understanding of English would be enhanced if we presented journal information and our review comments more clearly. This also entails writing shorter sentences.

The next post should discuss how the rest of the meeting goes and summarizes it.

 

 

 

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.

 

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