Research Remix

July 5, 2010

Evolution 2010 and iEvoBio recap

Filed under: conferences, openscience, Uncategorized — Tags: , , , , — Heather Piwowar @ 9:19 am

As my first exposure to the field of evolution, attending Evolution 2010 and iEvoBio was drinking from a firehose. That said, it was a productive and enjoyable dousing. Highlights:

Slides from presentations that highlighted open science, data sharing and archiving, and reward structures:

  • Mike Whitlock: Data Archiving in Evolution info session, discussed motivation and details on the joint data archiving policy that will require data archiving across six journals starting next year (policy, slides)
  • Carl Boettiger: My experiment with open science: Why the benefits of sharing go beyond source code, a dynamic practical case study of how and why to do open science (slides)
  • Todd Vision: The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem, motivation and overview for the new data repository for post-publication datasets in evolution and ecology (abstract and demo)
  • Rob Guralnick: Biodiversity Discovery and Documentation in the Information and Attention Age, keynote talk highlighting, in part, the value in sharing pre-publication data and the need to change our reward structures to value that contribution (slides)
  • Anne Thessen: New Biology: The Data Conservancy and Data Driven Discovery, an overview of the ambitious data conservancy project(website)
  • Jonathan Eisen: Phylogenomics of microbes: the dark matter of biology, keynote with some plugs for PLoS and project openness (slides)
  • Rutger Vos: TreeBASE2: Rise of the Machines, background on new machine-friendly interfaces to TreeBASE (slides) and demo

A few other presentations related to how we develop or communicate science:

  • Rod Page: Phyloinformatics in the age of Wikipedia, a talk on the value of realizing how people find science (slides)
  • Vincent Smith: Top-down and bottom-up informatics: who has the high ground?, powerful case studies of successful and unsuccessful projects (abstract)
  • Cynthia Parr: Community content building for evolutionary biology: Lessons learned from LepTree and Encyclopedia of Life, case studies on the relative strengths of different design approaches (abstract)
  • N. Dean Pentcheff: Copyrights and digitizing the systematic literature: the horror… the horror…, about why it is important and completely legal to assemble an open digital archive of phylogeny papers under fair use

We also had a very interesting iEvoBio Birds-of-a-Feather session on open science, data sharing and reuse, and data citations. There were about 10 of us in a wide-ranging and interesting discussion with diverse perspectives.

Overall the iEvoBio meeting was fun and useful: a very successful first year kickoff bringing together people with similar interests. Thanks to Hilmar Lapp and the other organizers for all of their work. Can’t wait to go next year and contribute to the theme of research openness.

Of course the meetings were also a very useful intro to the field of evolution itself. Sean Carron’s Gould prize lecture told the historical story of evolutionary theory: entertaining and informative, it was a fantastic start.  I also enjoyed the two award research lectures (though I wish they hadn’t overlapped with 5pm info sessions on Data Archiving and NESCent). The presentations and posters gave me a good high-level overview of what questions people are looking at, what kinds of data are produced and reused, what tools are developed, and what kinds of creativity and hard work required in designing effective experiments.

Finally, I made a number of contacts and spent some time with my NESCent and Dryad community, my local UBC community, and others interested in open data and open science within this domain… crucial given the remote nature of my postdoc.

Left now with oodles of disjoint notes, ideas, and enthusiasm for my next steps. Here we go!

ETA:  Want more info on iEvoBio?  Summary of online artifacts.

August 15, 2008

Does sharing information transform Researchers?

Filed under: conferences — Tags: , , , , , — Heather Piwowar @ 10:35 am

As you can imagine, a few months and an untold number of conferences makes for a lot of blogging fodder. The posts requiring new thought will have to wait, since I’m in the middle of a pilot-project crunch. But to get the ball rolling….

The ASIS&T conference looks very relevant to my research interests of data sharing and reuse. The special interest group SIG USE focuses on Information Needs Seeking and Use… definitely something I should check out. Consequently, I decided to apply for their PhD Student Conference Travel Award. The application required a statement that addresses “an issue relating to the current year’s conference theme in relation to information behavior research (how people need, seek, manage, give, and use information in different contexts).” This year’s ASIS&T conference theme is People Transforming Information – Information Transforming People. My entry statement is below, in case it is of interest.

People Transforming Information – Information Transforming People

Sharing information transforms Research –
Does sharing information transform Researchers?

Research advances when investigators build upon the results of others. This is possible whenever research results are shared at a sufficient level of detail to allow others to understand, replicate, critique, and expand on analyses; leverage is greatest when raw research data can be explored. Unfortunately, although shared raw research data has many benefits for the general research community, as yet there are few demonstrated benefits for the original investigators who bear the costs of making their datasets available.

I wish to evaluate the transformative effect on researchers when they share their data. Do they, as one might guess, receive more citations because their published results have an expanded usefulness? Do they become more aware of other available datasets, and thus more likely to reuse shared data in the future? Do they become more likely to embrace other mechanisms, such as publishing through open access models, for making their research results widely available?

I am engaged in a long-term effort to identify instances of research data sharing and reuse. I plan to address the above questions, and others, by looking at publication patterns, covariates, and data-sharing behavior of various research communities. Through this work, I hope to quantify incentives for researchers to share their data, identify synergies between open access and open data, and highlight the need to evaluate policies and behaviors to realize the full potential of our research activities.

Travel award winners to be announced at the SIG USE symposium in October.

March 24, 2008

Preprints of conference submissions?

Filed under: Open Notebook Science, Policies — Tags: , , , , — Heather Piwowar @ 12:45 pm

It continues to surprise me how hard [1, 2] it is to figure out the rules for publishing in most journals, particularly with respect to preprints. I’m finding the policies for publishing in conferences are just as ill-defined. This is a shame because it surely decreases sharing.

I’ve been putting my work up on Nature Precedings. I submitted a poster a few days before the ISMB conference. Nature Precedings asked me if I knew whether ISMB would permit this. I emailed to ask: they quickly responded that it was no problem. I’ve since asked PSB and ELPUB: again, no problem. I think that ELPUB did make state this during in the submission process, but in all three cases it would be great if they wrote this explictly on their websites so that people could feel free to post and discuss draft submissions… I’ll send a few emails to suggest it.

I recently asked AMIA. I was pointed to the contributor license agreement [below], which left me guessing. What does “publish” mean? For most publishers I’ve talked to it means “published in an official capacity” and they don’t count blogs or pre-print servers. Yet clearly the journals who disallow preprints disagree with this definition [quick list for Clinical Medicine, or Sherpa/RoMEO for an extensive list]. JAMIA, the official journal of AMIA, does not allow preprints. So I guess I should email AMIA again and ask for further clarification.

ETA:  I emailed again and quickly got a very clear response: Preposting is fine so long as the other sites don’t formally publish the work.”   Great news, thanks AMIA.

I’d like to “ask for forgiveness rather than permission” but the potential down-side is too great in this case. Student publication in AMIA is highly-valued in my department.

I wonder if author copyright addenda can apply to conference submissions??? I don’t see why not. Will have to keep that in mind next time.

AMIA Annual Symposium 2008 license agreement:


February 8, 2008

Letter of support for PSB session on Open Science

Filed under: Uncategorized — Tags: , , , — Heather Piwowar @ 7:48 am

Posted here under under Creative Commons license, so please reuse, remix, re-send!

Dear PSB organizers,

I fully support the proposal for a session on Open Science at PSB 2009, and commit to submitting a research paper on data sharing and reuse.

The specific research topic will be derived from my doctoral dissertation, related to measuring the prevalence, patterns, causes, benefits, and motivations for biomedical data sharing and reuse.  I have a previous publication in this area (“Sharing Detailed Research Data Is Associated with Increased Citation Rate” at PLoS ONE), a few posters (including one at PSB 2008), and several papers in draft.  The paper will be co-authored with Dr Wendy Chapman.

I believe that Open Science definitely constitutes a “hot topic” within biocomputing, and has the potential to fundamentally change the way we think about our work.  The topic is relevant to data producers and data consumers, biologists and computer scientists, all with varied perspectives.

Discussion and measurement of benefits, hurdles, progress, and best practices could (and is) taking place in blogs, the popular press, Birds-of-a-Feather sessions, and scattered research papers.  A session at PSB would be a unique opportunity to give this emerging meta-approach the serious examination it deserves.

Thank you for considering this proposal.


Heather Piwowar
Doctoral Student
Department of Biomedical Informatics
University of Pittsburgh

February 7, 2008

Plug for PSB Session on Open Science

Filed under: Uncategorized — Tags: , , , , — Heather Piwowar @ 10:07 pm

Hi Blogosphere!  I’ve missed you.  Hope to re-engage in the next month or two.   Briefly in the mean time….

I want to offer public support and a last-minute plug: Shirley Wu and Cameron Neylon are proposing a session on Open Science at next year’s PSB meeting.  Fantastic idea.

You can help… if you’d like to attend and/or submit a presentation, please send them a letter stating such by tomorrow noon PST.  Details here.

I’m sold.  PSB is a first-rate conference, it would be a unique opportunity to bring together perspectives on Open Science developments, I’d love to meet others in the community, and yup… it is in Hawaii in January.

Off to write my “I’ll definitely submit a research paper on data sharing and reuse” email,


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