http://blog.openwetware.org/programmablecells Cells compute - Let's program them. Thu, 17 Apr 2008 16:04:06 +0000 http://backend.userland.com/rss092 en There has been a lot of discussion about how OpenWetWare can best get involved with scientific publishing. One of the ideas that has been tossed around is to develop OWW as a place to publish supplementary material. In the spirit of my ongoing experiment with OWW as a ... http://blog.openwetware.org/programmablecells/2008/04/14/openwetware-and-supplementary-material/ This is the fifth report of the 'Publishing on OpenWetWare' series. In brief, I am writing an article on OWW from start to finish: initial writing -> collecting comments -> publishing on arXiv.org -> presenting at a conference. For other articles, see one, two, three,four. In this ... http://blog.openwetware.org/programmablecells/2008/03/15/publishing-on-openwetware-lessons-learned-4-presenting/ This is the fourth report of the 'Publishing on OpenWetWare' series. In brief, I am writing an article on OWW from start to finish: initial writing -> collecting comments -> publishing on arXiv.org -> presenting at a conference. For other articles, see one, two, and three. In ... http://blog.openwetware.org/programmablecells/2008/03/15/publishing-on-openwetware-lessons-learned-3-wikitolatex-and-publishing-on-the-arxiv/ This is the third report of the 'Publishing on OpenWetWare' series. In brief, I am writing an article on OWW from start to finish: initial writing -> collecting comments -> publishing on arXiv.org -> presenting at a conference. For other articles, see one, and two. In this ... http://blog.openwetware.org/programmablecells/2008/03/10/publishing-on-openwetware-lessons-learned-2/ Previously I wrote about my plan to try out OWW as an authoring platform. I have now completed the first phase of this little experiment, and I thought I would share my experiences. The first draft of 'Python - All A Scientist Needs' can be seen here. I wrote ... http://blog.openwetware.org/programmablecells/2008/02/20/publishing-on-openwetware-lessons-learned-1/ The Steering Committee has been talking about developing an alternative publishing system/model through openwetware. I wish I could give a more concrete definition of what we are trying to achieve, but we are still in a pretty active debate and nothing clear has emerged. My personal opinion about it, is ... http://blog.openwetware.org/programmablecells/2008/02/07/publishing-on-openwetware/ The past month or so I have been moving from Ithaca, NY to Berkeley, CA, and I am happy to have arrived at my new home in the Arkin Lab. I'm still in the process of settling in, but I have managed to start experiments thanks to John Dueber ... http://blog.openwetware.org/programmablecells/2008/01/15/my-new-home/ I owe another thanks to Bill Flanagan for installing the WordPress markdown pluggin, which enables me to format my posts in markdown rather than in HTML. This really makes writing blog entries much more fun and convenient since now I can easily use TextMate to write my entries offline at ... http://blog.openwetware.org/programmablecells/2007/11/04/blogging-with-textmate-and-markdown-implications-for-open-lab-notebooks/ I cannot resist mentioning something that I think will really add another huge boost to the open science movement. arXiv.org has now opened up its massive troves of open access articles via an Application Programming Interface, or API. You might think that you have never heard of arXiv.org before, nor ... http://blog.openwetware.org/programmablecells/2007/10/25/announcing-the-arxivorg-api/ Topic Whole-cell biocomputing, by M. L. Simpson, G. S. Sayler, J. T. Fleming and B. Applegate out of Oak Ridge National Lab, University of Tennessee and Purdue University. Open Access Journals This paper is published in Trends in Biotechnology by the scientific megapublisher Elsevier. It is a shame that this article is not available ... http://blog.openwetware.org/programmablecells/2007/10/04/journal-club-whole-cell-biocomputing/