As usual, I have been recklessly following many lines of thoughts and opening many tabs in my browsers (I use two browsers so as to try to cheat or at least confuse the sites using cookies to learn more about me than I know myself), and now I am in the middle of crashing my machine and loose all the links from the open tabs… So here I am on my netbook to keep a record of where I was so I recover somewhat.
[I still don’t know a good way to use browser(s) as research tools and ensure I can followup searches and links. There was a time I was using Delicious to keep track of interesting links, but then I never had time to go back and revisit unfinished business and so have abandoned this, and rely on keeping tabs open until I get to the information.]
So what are some of the tabs I will be losing in a few minutes? (Chrome has just displayed a “He’s dead, Jim!” message.
-Two of them are about serious games, one about work at SRI and USCS’s development of Xylem to gamify software verification, and another which is about Ero.Coli, a game to explore Synthetic Biology. Maybe I will try to play these over the break!
– One tab is displaying an e-book of SFM 2008, LNCS 5016, Formal Methods for Computational Systems Biology, a great collection of tutorial papers. I was specifically reading the chapter by Carolyn Talcott on Pathway Logic. I got to this chapter via searches for the MAPK Pathway. This is a system that many computational biologists have been studying, and I am looking at it specifically because I wanted an example where intra-cellular locality is important. For the MAPK pathway, some activities take place at the celllular membrane, other in the cytoplasm, and finally the action on controlling intra–nuclear activities leading to cell division. The wikipedia page is quite good. My student Faiz is looking for examples which depend on intra-cellular localization.
– A further tab is open at the my lecture slides for Operating Systems, while I was answering student questions. I’ve enjoyed teaching OS, but need to make changes if I am teaching it again next year. Silberschatz et al textbook is quite good but probably too extensive for a 18-lecture module. I will try to look for a more succinct and focused book.
– I am looking at Session Types. My colleague Andrzej suggested I look at them as ways of representing concurrency between different metabolic pathways. It seems intriguing, and I definitely want to look for papers on this, once my computer is rebooted and ready to go.
– One tab open on llnl’s Visit visualization tool. It looks great as a away to simplify the visualization of outputs from simulation. I will try to run this on my netbook. The only problem I have with it so far is… why call it *Visit*?? What an un-searchable name! Please use imagination to give it a unique and interesting name!
– One tab opened on Microsoft Research’s DNA Strand Displacement Simulator. Really interesting work. Another tab open at Lakin and Phillips preprint of paper to be presented at PADL; very nice approach.
– A tab with Baianu’s paper on Lukasiewicz Algebras – I still don’t understand categorical frameworks, and don’t know how much time I will invest in detailed mathematics, but nevertheless something to keep for future reference.
– It’s not all work: I have a tab looking at the Guardian’s bike blog’s page on winter cycling clothing. I confess I have become too soft and I don’t ride my bike in winter, but that is mostly because of the dark rather than the cold.
While I was writing the above my linux box crashed and restarted, I am sure I lost some information. However, I hope this gives anyone interested some information on the kinds of things that have been interesting me this week, when I get to dedicate myself to research after the end of term and before the Christmas festivities take over.