0Chris Morgan's Wiki Page
- Run through Misha's flow chart with one of the datasets. Ask either of us for clarification/details.
- Looks to me like you should use the simpure data set for testing, since using the real150 dataset will require additional knowledge about the data in /home/hiv
- Write script to run through flow chart on one fixed dataset automatically.
- Transfer this script and all related files to cirilo and run it through the web. Then deliver the results file to the web.
- Check PubMed for any recent publications about viral genotyping tools.
- Learn background: NCBI tool, REGA, CART, BART
- Learn Misha's code and data sets: Misha's writeup
- GenotypingWebPage: goal is to set up a web server to perform genotyping
- Existing genotyping tools:
- REGA (I think, although they claim there is yet no publication about this tool.)
- BART R package
- rpart R package for CART (newest version straight from McCulloch website )
- HTML editors (for making static webpages): Windows: Frontpage, Linux: Quanta, Bluefish, Ginf, Screem, Nvu, Mozilla Composer (if you choose one and want it installed on cirilo, le me know)
0Recent PubMed Publications on Viral Genotyping Tools
- Researchers in Bulgaria used REGA to analyze HIV-1 here need ncbi link, this one doesn't work without a cookie
- Phylogenetic data used to develop molecular tools for genotyping Yam Mosaic Virus (used variety of primers and PCR) here