Based on user suggestion we launch series of posts based on ideas promoted by the Uses This website.
How are the tools that we use every day being developed? What do bioinformaticians with proven track record use to get their work done?
I have sent out a few emails and I will start posting answers as they come in. Feel free to send me candidates (or volunteer) for the interviews.
Jim Robinson of the Integrative Genomics Viewer
What hardware do you use?
Development is done primarily on a MacbookPro
What is your text editor?
I develop code in the Intellij IDE. When editing plain text I often use TextWrangler.
What software do you use for your work?
Intellij, JProbe, JFormDesigner, Apache web server, Charles Proxy, SmartGit, Chrome developer tools, Firefox developer tools
What do you use to create plots and charts?
For Java Swing and the AWT. For the web primarily canvas.
What do you consider the best language to do bioinformatics with?
Whatever works for you
What bioinformatics tools/software do not get enough recognition?
See all posts in this series https://www.biostars.org/tag/uses-this/
To be notified of new post in the series follow this post.
Are you taking requests? Jim Kent!
I'll try ;-)
I would love to hear from a member of the Galaxy team. Given your workplace you should have easy access to them, correct?
Also, more from the team at the Broad!
New entry: Aaron Quinlan of Bedtools uses this
New Entry: Jonathan Pevsner author of Bioinformatics and Functional Genomics uses this
New entry: James Taylor of Galaxy uses this
New entry: Heng Li of BWA and Samtools uses this
New entry: Ruibang Laurent Luo of SOAPdenovo uses this
New entry: Robert Edgar of USearch and MUSCLE uses this
New entry: Hadley Wickham of ggplot and RStudio uses this
New entry: Mary Mangan of OpenHelix uses this
New entry: Ann Loraine of the Integrated Genome Browser uses this
New entry: Obi and Malachi Griffith of DGIdb use this
New entry: Martin Frith of the LAST aligner uses this
New entry: Daniel Huson of MEGAN and Pauda uses this
New entry: Pablo Cingolani of snpEff uses this
New entry: Bob Harris of the LASTZ aligner uses this
New entry: Kai Wang of Annovar and PennCNV uses this
New entry: Ryan Poplin of GATK uses this
New entry: Daniel Zerbino of Velvet and Oases uses this
New entry: Brian Haas of the Trinity Assembler uses this
New entry: Tao Liu of MACS uses this
New entry: Pat Schloss of Mothur uses this
New entry: Cole Trapnell of TopHat and CuffLinks uses this
New entry: Nils Homer of BFAST and Picard uses this
New entry: Erik Garrison of FreeBayes uses this