Monday, February 25, 2008

NFAIS 2008 Sunday afternoon

Yesterday afternoon I attended the NFAIS conference in downtown Philadelphia. The talks were actually very engaging.

First up was David Weinburger, who co-wrote the "Cluetrain Manifesto", an enjoyable book that I caught on audio book a few years back. His talk was mainly about his new book "Everything is Miscellaneous", which looks interesting based on his talk. His main point was that hierarchical classification systems are not as useful for many systems compared with spontaneous tagging by online communities. He also indicated that information overload was not as big of a problem as many people suggest, something that I definitely think is the case in science.

Lee Rainie's presentation was also well done. He presented the results of the Pew Internet & American Life project. I thought the most interesting portion was at the end, where he described the 10 different types of people, classified according to their attitude towards technology. Hopefully his report will be available shortly along with the rest. (In the meantime, Bryan Alexander took some good notes on this session.)

I presented at the next session on "The Emerging Culture of the New Information Order" on Open Notebook Science, which was a good fit, giving a laboratory researcher's perspective of Web 2.0.

My co-panelists included Chris Willis from and Bryan Alexander from NITLE. Chris gave many good examples of the power of community tagging, including a new project bringing relatives of Vietnam veterans together on a massive digital "wall". Bryan also gave a stimulating talk but he was so addicted to his social software that he was recording video blog posts as we were waiting to speak :)

Tuesday, February 19, 2008

Scholar 2 Scholar Meeting at Drexel

I am co-organizing the Scholar 2 Scholar conference with Jay Bhatt and Anita Chiodo on the morning of April 16, 2008 at Drexel University in Philadelphia. Anyone wishing to attend add your name to the participant list on the wiki.
Drexel University Libraries’ Scholarly Communication Symposium
Scholar 2 Scholar: How Web 2.0 is Changing Scholarly Communication as We Know It

Web 2.0 technologies are more than just web-based games and social networks; these virtual environments are building communities of thought and practice which have very real implications for education and research in academia. How do educators, administrators, and librarians use or repurpose these tools to their advantage? What are the implications for teaching and research? Is the return on our investment of time and energy worth the engagement? How well do students learn through these collaborative avenues? What are the true benefits for scientific research? What are the potential conflicts or roadblocks? We will explore these questions and many more.


Monday, February 18, 2008

Open Medicine Editorial on Open Science

The Journal "Open Medicine" has published a very thoughtful editorial on "Open science, open access and open source software at Open Medicine" by Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk and Anita Palepu.

Not only are they writing about it but they want to get their hands dirty as well:

Open Medicine is an open access journal because we believe that free and timely access to research results allows scientific knowledge to be used by all those who need it, not just those who can afford expensive journal subscriptions or user fees for individual articles. But is access to the final polished version of research enough? Could we do more to en­courage the collaborative reuse and reanalysis of existing data, or the verification of analyses? Could we move from open access to open science?

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Wednesday, February 13, 2008

ACS Island on Second Life

The American Chemical Society will be offering a virtual poster session in Second Life from selected posters at the Sci-Mix session taking place April 6, 2008 at the next national meeting in New Orleans.

I'm helping out with that effort and I'm pleased to say that we have our first submission from Jodye Selco, Mary Bruno and Sue Chan: "Safe and economical chemistry inquiry for the K-12 classroom".

ACS island has the same shape as its logo of a phoenix, thanks to the skilled hand of Eloise Pasteur who carved out the Drexel island's dragon shape. The posters will be placed on the right wing, next to a "chemistry museum" area, also under development.

ACS island is currently open to everyone - feel free to stop by and explore as we develop the area (Andrew Lang, Hiro Sheridan in SL is also on the project). Gus Rosania has been a very active "resident scientist" - you can see his activities on drug transport near the middle.

Kate Sellar (Finola Graves in SL), who spearheaded this initiative at ACS, has just started a blog where she will chronicle activities on the island.

The easiest way to find the island is to type ACS in the Map search box in Second Life.

Thursday, February 07, 2008

Open Notebook Science News - Barton and Rosania

Michael Barton has posted a brief essay on Open Notebook Science on his research web site:
As you might expect from the name, Open Notebook Science (ONS) has similarities with Open Source Software. The clearest likeness between the two, is the belief that by sharing and collaborating, more can be achieved than through secrecy and competition. An open approach to software development is proven to be successful: the greatest achievement is the development, and increasing adoption of the Linux operating system. On this foundation other applications like the Apache web server, MySQL database, and the PHP scripting language have been built, and the combination of the four is the engine running many websites, including this one. If ONS can enjoy a fraction of the success open software does, then science can only benefit.
He also discusses ONS on the February 2008 edition of Bio::Blogs.

In terms of an amazing example of recent ONS implementation, take a look at Gus Rosania's 1CellPK wiki. He currently has 9 of his group members with notebooks and he is trying to make the activities in his lab as transparent as possible. Obviously this involves experiments but also group meetings and his meetings with colleagues. He has also been providing detailed descriptions, including background and literature reviews, of his group's projects.

Of particular interest to my group is the description of our collaboration on new anti-malarial agents. Since we can track their activities and they can track ours in close to real time, it will be interesting to see if we can crack open all the black boxes of collaboration.

I have heard the objection many times that there is not enough time for researchers to read each other's lab notebooks. That's absolutely true but that is not an effective way to use these resources. The point is to spend little time skimming content and as much time as required drilling down to details when a relevant post is discovered. With Wikispaces one can also just subscribe by email or RSS feed to edits of a particular page. I would expect the UsefulChem group members to at least subscribe to the malaria project page I mentioned above.

Gus is also looking at displaying experimental results in Second Life and has been doing actual experiments on the physics of Second Life. See his blog for the chronicles of that adventure.

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Tuesday, February 05, 2008

Open Science Session at PSB

Shirley Wu is organizing a session at the Pacific Symposium on Biocomputing (PSB) 2009 in Hawaii.

"Open Science: tools, approaches, and implications

She is looking for submissions, support and feedback:
So if you would like to support this proposal and are willing to commit to participating should it get accepted, please send me an email to that effect (with as many details of your anticipated participation as you can provide at this time), and I will include all the emails as "supplementary material" next Friday. Please also disseminate this call on your own blogs if you can. Many thanks in advance!


Opening Up the Black Boxes of Science

Here is my first post for Just Science week.

Collaboration is a requirement for the advancement of modern science. Researchers cannot be expert at everything and must specialize to make a unique contribution.

But if coordinating research within a group is challenging, effective collaboration between groups is even more so.

There is often a strong temptation for research units to treat each other like black boxes. There is some logic to this - the point of having a collaborator is to distribute the responsibility of tasks in a project. If I get involved with every detail of my collaborator's work I may as well do the work within my own group.

But problems can arise because of unstated assumptions between groups. A good example is a recent collaboration with groups testing for biological activity. We synthesized compounds and shipped them out for various tests (anti-tumor and malarial inhibition). The researchers performing the assays may have assumed that we had verified aqueous solubility and we didn't think of it since we were not familiar with their protocols.

In all of those cases, the compounds were taken up in DMSO then diluted into an aqueous medium (anti-tumor, falcipain-2 EXP165, Plasmodium EXP166). I would guess that the solubility of most of these compounds in water is very limited, in which case the activity would be under-reported, with most of the product precipitating on the walls of the reaction vessel, floating on the surface or clumped up in suspension.

Now that we know this we can make a point of measuring the aqueous solubility in our lab to make sure that the intended concentrations can be achieved during testing.

It is quite possible that some collaborators will perform such a solubility test as a standard part of their complete protocol. But there is no way to know that without groups interacting at a detailed level.

Lots of discussion is one way to get there. Using Open Notebook Science can be another convenient way of avoiding erroneous assumptions in a collaboration. Not everything needs to be read but it can be accessed if there are doubts from any of the parties.

As I mentioned previously, we can make sure our compounds are water soluble by including an amine. Primary amines are problematic since they participate in the Ugi reaction and we have had problems with tertiary amines.

Including boc-protected amino acids as the carboxylic acid component has a few advantages. First we know that we can make and isolate them successfully. Second, these are readily available commercially since they are building blocks for polypeptides.

Seeking to keep with simplicity and speed maybe we can just shake up the boc-protected Ugi product powders with 85% phosphoric acid until dissolved then dilute up with a near neutral phosphate buffer and ship out those solutions for testing directly. Phosphoric acid has been reported to cleave boc groups in a few hours at room temperature. Phosphate buffer should be compatible with most of the biological assays.

For example (from EXP097):

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