Martin Frith is a computational biologist working at the Computational Biology Research Center of the National Institute of Advanced Industrial Science and Technology in Japan. The CBRC is on the island of Odaiba, a futuristic entertainment district near central Tokyo.
Dr. Frith is the author of several software packages among them the LAST aligner that embodies the most recent advances in the field. With the LAST aligner fast chromosome-wide alignments can be performed on human size genomes even with low computational resources.
We have asked Dr. Frith on his journey to being employed at CRBC. He said that he likes living in different countries. He started his career in England, went to China for a few years, then USA for several years. He did a postdoc going back-and-forth between Australia and Japan, then decided that he liked living in Japan the best. For now.
What hardware do you use?
Apparently I'm using some PC with Intel core i7. I don't think about it much. I have a Mac Air too. And I use my Center's medium-size Linux cluster.
What is your text editor?
Emacs (not an informed choice: I never really tried any others).
What software do you use for your work?
One non-obvious one is GNU parallel.
What do you use to create plots and charts?
R. (Not because I think it's best, but because R seems popular for various things so I want to learn it a bit.)
What do you consider the best language to do bioinformatics with?
Unix shell (when you don't need to implement an algorithm, for combining other tools). When you do need to implement an algorithm, Python is best. Huge caveat: I haven't tried most languages. I'm only considering extremely mainstream ones.
No doubt Lisp is really the best.
What bioinformatics tools/software do not get enough recognition?
- My tools! (In particular tantan, the only low-complexity masker that actually works. Best thing I've done.)
- ALP: statistical parameters in the modified Gumbel distribution for BLAST
- Vmatch: large scale sequence analysis software (pity it's closed-source): http://www.vmatch.de/
- Iedera: Iedera :: subset seed design tool http://bioinfo.lifl.fr/yass/iedera.php
- Rtools: Bioinformatics Web Server for RNA http://rtools.cbrc.jp/cgi-bin/index.cgi
- LAMP: limitless-arity multiple testing correction http://a-terada.github.io/lamp/
Surely many others too.
See all post in this series https://www.biostars.org/tag/uses-this/
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