Thursday, March 29, 2007

ACS Chicago - Day #3

Tuesday promised to be an interesting day: an interesting 'Scientific Communication' CINF session in the morning and early afternoon. And, rather important to me, the Blue Obelisk dinner that night, just after another CINF party, where I chatted with a few others about options of a chemistry equivalent of the Google Summer of Code; who knows what happens this summer, but start thinking about ideas on how to increase the web experience of chemistry journal web pages.

The GSoC
Now that I am talking about the GSoC, you might have realized that the CDK and Bioclipse did not make it as mentoring organization. While I had not seriously expected it, all the enthusiasm from within both projects including several interested students, I was a bit hoping for getting accepted with at least on of them. Meanwhile, KDE, as expected, is approved, and actually contains two interesting chemistry project ideas too. One is about a 3D viewer/editor for which 7 students send Google a proposal, and the other about text mining of chemical content on the desktop, using Strigi (two students). Both topics have one excellent proposal, who do good in the ranking process. So, we might have some chemistry in the GSoC afterall.

OK, back to the ACS meeting. Fahrenbach had a presentation on blogging too, but don't remember anything special about it. The CHED session was more elaborate on the whole topic, and since you are a reader of chemical blogs, you all know about this anyway :) Loney introduced which is building a social network around biotechnology. There are other community sites like this, and my major problem with these community building efforts is that they are too well defined. I much prefer to work in a more open environment where I can get in contact just as easily with people outside some specific topic. For the rest, the set of technologies is rather comprehensive.

Frenkel spoke about the imminent success of ThermoML, which is now being supported by vendors and publishers, smoothing the whole dissemination of data supported by this format. It is basically what CML is attempting to achieve in molecular structure data. Day is having a good go at this with crystal data, and his CrystalEye project is supposed to be launched next month.

Hey, at, had a rather manager level presentation, with very little value for someone into the field of 'data lifecycle and curation'. Rather disappointing on a scientific conference, or am I judging the ACS conference here? If the Microsoft is getting interested in chemoinformatics that might be a good thing, as long as the are OK with open source, open data and open standards. Who knows...

Rzepa had his presentation on the semantic wiki, which he, in similar form, held at the German Chemoinformatics Conference too. New, I think, were the sheets on reasoning based on the content of the wiki. That was rather interesting. If we all would make our chemical knowledge available as RDF, then this can become a big thing very soon. I skipped the presentation of Renear on ontologies, though it was actually one that I had hand picked; but I was simply too tired. Will watch the podcast when available. (BTW, are they making podcasts for the CINF session only, or for the whole ACS meeting?)

In the afternoon, I also followed just a subset of the presentations. The last one was by Scott who spoke earlier on Second Life. I'm really interested in seeing where this is going, though I have my reservations if this is the right medium for mining chemical knowledge. Today she spoke on the social bookmarking and podcasting initiatives at Nature and Nature Network. The latter is a social site, like like BioTechExchange, but not limited to one specific topic, and more interdisciplinary (my account at NN). I blogged about some early issues some time ago.

Jabri showed us how Jmol is adding value to the ACS Chemical Biology journal. Yes, that's what she said. An opensource tool, developed by people on their free time, is making an ACS journal more valuable. I am very happy to hear that, and it strongly supports our view that opensource chemoinformatics is very important. Some more support from established organizations might be in order indeed!

Blue Obelisk
It has become a habit to organize Blue Obelisk dinner to talk about opensource, opendata, openscience, and the future. Actually, we secretly talk about talking over the world, but I can't say that. (Neither can I tell anything about our secret rituals. The protocol for becoming member of our society is quite simple though: be clear about your opinion that ODOSOS is the future.) Dinner was great, and it was great talking to several older and newer members of the movement. Cheers all! Oh, there also was some awards involved, but I hope Peter and Christoph will blog about that and post the pictures.


  1. It's too bad that my presentation was not able to crystalize anything in your memory, but no matter. I will just tell you again right now :) It was the second time I've ever presented anything before, so granted there is more room for improvement. But thanks for the feedback! This is exactly one of the reasons blogs are so cool. It helps me know what people are thinking.

    One of the things I meant to instill in your memory at the ACS was this social network site I constructed not just for scientists, but for academics in general that incorporates the use of collaborative software for greater sophisticaion of interaction between the users on the site. I agree with your comment about there being a need for social network sites to be realy inclusive of a lot of different disciplines, not just one or two. Diversity of the user base is what gives such sites their value. The URL is o2hu stands for "online office hour university." I'd appreciate it if you would check it out, and if I can convince you further please take two minutes to register.

  2. The current line I've heard from Microsoft on Open Source is that they're happy with BSD, but not with copyleft (GPL).

  3. Jim, sure, because BSD allows them to do anything with it what ever they like... without having to worry about contributing to the community. The GPL, however, explicitly disallows lurking, which makes some sense. CDK, Jmol uses LGPL which allows embedding in proprietary systems too, just like BSD. Any idea on the position of MS towards LGPL?

  4. Albert, sorry about that. I was a loosy comment maker this conference. Last week has been quite chaotic, but I plan to write up another blog item about the ACS meeting, and I will try to remember o2hu,

    BTW, any idea how and when the podcasts will be available?