Science Blogging Conference: Post 3 Open Source/Open Notebook Science
Jean-Claude Bradley, Drexel, http://usefulchem.wikispaces.com/

(not open source software in science, but open notebook science)
(not blogging about an article, but the blog is the article)

Issues
- intellectual property
- referencing and claims to priority
- academic validation
- peer review – mandatory and elective

Opportunities
- more publishable work, not less, because smaller units and cross discipline work that doesn’t have a home
- making explicit the work in collaborations
- more detailed knowledge base
- using semantically rich format and automation…

Robot scientist

How will this happen?
- open source either author pays or reader pays… needs freely open where no cost to submit and no cost to read (like free hosted systems like Blogger, etc.)

What they did/are doing
- google to see what’s needed
- asked Find a Drug for information
- synthesized molecules and documented on blog
- got real comments

Found
- time stamping not as reliable since it can be changed
- if things are changed, then old info is lost
- use a wiki to gather information and a blog for their molecules

Details
- site meter, knows what people are searching for and who’s reading
- use free, hosted software so all of this can be replicated

Automation in Useful Chem
- smiles and InChI through Chemsketch
- useful chemistry molecules

• see in Jmol
• smiles
• InchI
• Searches emolecules (used to be chmoogle)
• Data, not just pictures

Others connected
- Synaptic leap
- ChemRefer
- Partnerships with English classes and undergrad chem.

Other findings
- Blogs best as an integrative tool
- Graphical Mining of data with JSpecView – java view of spectra where you can actually zoom in on an important area, exporting in a CML format so machines can use
- vendor reliability
- classical long tail – there is only a very small audience for this information, so even though not wide readership, is it reaching who needs to read it

Others
- org prep daily
- open webware – protocols, lab notebooks for intra-group communication (not enough context to allow external people really to communicate)
- RRResearch.blogspot.com (microbiology)
- Chem.-bla-ics – actual code

Comments from the audience (c) and responses (r)
(c) I’m an astronomer, and I do my observations two nights and spend the next few months doing the work – if I publish my data, then someone might scoop me and worse, the work I had planned as follow-on… the data is usually embargoed
(c) I’m in the same boat, you can generate the data very quickly but the analysis takes a long time
(c) What’s your opinion of colleagues who try this? Maybe they won’t get hired.

(r) The open source will beat the traditional publishing to publishing all of the time

(c) can you actually publish this work?
(r) talk to editors, and they say yes, regardless of what written policies say

(c) what would you change with this software if you could to improve this work
(r) they’re all separate programs which is good… we’d like to be able to show more spectra on the same java graph

(c) how do you deal with vandalism?
(r) he’s never had it happen – also don’t have to have it fully open for editing

(c) ada compliant? Universities are required to follow that…
(r) he hasn’t had to deal with this

(c) do you recognize your commenters from references, etc?
(r) frequently in person or via e-mail and then get permission to post that to the blog.
(r) the community of researchers doing the same work is pretty small so you probably know them
(c) but do you ever actually get people from out of the blue
(r) preservation of old data so you might not be in the field later but

Actually have spectra from starting material so will know about impurities, etc.

(c) relative merits of self archiving vs. submitting to open data archives
(r) we do both and whatever is available

(c) do you find new collaborators through this
(r) I didn’t know any of these people before this because I came from nanotechnology, so I’ve met a lot of people – especially

(c) use this for grant applications?
(r) not yet, but will

(c) could you do this with a high value drug – would your university let you?
(r) universities don’t push to patent [depends on the university!], but this works as marketing for the university to bring new students

(c) is your management supportive?
(r) yes, very and we have openings!

Labels: sciencebloggingconference

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