Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
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gravatar for Istvan Albert
4.3 years ago by
Istvan Albert ♦♦ 78k
University Park, USA
Istvan Albert ♦♦ 78k wrote:

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?
bedtools


See all posts in this series https://www.biostars.org/t/uses-this/

To be notified of new post in the series follow this post.

uses-this forum • 4.8k views
ADD COMMENTlink modified 4.3 years ago by Obi Griffith17k • written 4.3 years ago by Istvan Albert ♦♦ 78k
3

Are you taking requests? Jim Kent!

ADD REPLYlink written 4.3 years ago by Madelaine Gogol5.0k
1

I'll try ;-) 

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k
1

I would love to hear from a member of the Galaxy team. Given your workplace you should have easy access to them, correct?

ADD REPLYlink written 4.3 years ago by Dan D6.7k
1

Also, more from the team at the Broad!

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Dan D6.7k
1

New entry: Aaron Quinlan of Bedtools uses this

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Istvan Albert ♦♦ 78k
1

New Entry: Jonathan Pevsner author of Bioinformatics and Functional Genomics uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k
1

New entry: James Taylor of Galaxy uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k
1

New entry: Heng Li of BWA and Samtools uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k
1

New entry: Ruibang Laurent Lo of SOAPdenovo uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k
1

New entry: Robert Edgar of USearch and MUSCLE uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k
1

New entry: Hadley Wickham of ggplot and RStudio uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k

New entry: Mary Mangan of OpenHelix uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k

New entry: Ann Loraine of the Integrated Genome Browser uses this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k

New entry: Obi and Malachi Griffith of DGIdb use this

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 78k

New entry: Martin Frith of the LAST aligner uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Daniel Huson of MEGAN and Pauda uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Pablo Cingolani of snpEff uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Bob Harris of the LASTZ aligner uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Kai Wang of Annovar and PennCNV uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Ryan Poplin of GATK uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Daniel Zerbino of Velvet and Oases uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Brian Haas of the Trinity Assembler uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Tao Liu of MACS uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Pat Schloss of Mothur uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Cole Trapnell of TopHat and CuffLinks uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry:Nils Homer of BFAST and Picard uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k

New entry: Erik Garrison of FreeBayes uses this

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 78k
3
gravatar for Mary
4.3 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Terrific idea for a series, Istvan. Funny, I just talked with Jim last week and learned about his heavy-lifting on the IGV tools. Amazing work from a comparatively small team (compared to other genome browser teams).

ADD COMMENTlink written 4.3 years ago by Mary11k
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