People - perm - Efficient mapping of short sequences accomplished with periodic full sensitive spaced seeds

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Project People

Name	Role	Duties	Notes
Chen.Yan...@gmail.com	Owner	Design core libraries, write code and unit tests Plan the scope of release milestones and track progress Set up and maintain build tools and test automation Specify and write code for APIs and plug-in interfaces Triage new issues and support requests from end-users	This is Yangho. I graduated as a PhD student from Prof Ting Chen's lab at the University of Southern California. If you have any question or suggestion about PerM, please contact me dirrectly. Thank you for using PerM.
phdc...@gmail.com	Owner	Lead by providing a project vision and roadmap	Professor Ting Chen is our brilliant adviser who guides us in developing the core algorithm. With his idea about Integer Programming reduction, we found the periodic seed that could be full sensitive to different sensitivity levels. It is because his insight and much critical thinking about the data structure and design so we can publish the paper.
tade.sou...@gmail.com	Owner	Develop and refine Algorithms Develop tools for downstream analysis Lead by providing a project vision and roadmap Triage new issues and support requests from end-users Write end-user documentation and examples	Tade and I were partners in the design of PerM. His algorithmic contributions included the development of periodic seed extension to variable length. This idea significantly reduces running time for large reference genomes. He is currently developing SNP calling software to accompany PerM. H
zach.fra...@gmail.com	Owner	Design new features, write code and unit tests Lead the UI design and incorporate feedback Measure performance and find bottlenecks to optimize	Zach is working on further increasing the utility of PerM as well as developing downstream SNP calling tools to accompany PerM.
ying.wan...@gmail.com	Owner	Test the system before each release	Dr. Wang is a professor in Xia-men university. I appreciate her great help in testing PerM on the brain RNA-seq reads data to many different data sets.
matthew....@gmail.com	Committer + DeleteIssue	Document our development process and help new members Measure performance and find bottlenecks to optimize Write end-user documentation and examples	Dr. Kidd is a bioinformatician and the CIO of GHC Technologies, a business unit of ICx Technologies (soon to be part of FLIR Thermal Imaging). He is currently developing biodefense and metagenomics applications.
sungje....@gmail.com	Contributor + CreateDownload + DeleteDownload + DeleteIssue + EditAnyDuties + EditDownload + EditIssue + EditWiki	Test the system before each release	Sungie helps me in testing the program and compared with the read assembly for RNAseq with his program.
misagh.b...@gmail.com	Contributor + CreateDownload + DeleteDownload + DeleteIssue + EditDownload + EditIssue + EditWiki	Develop tools for downstream analysis Document our development process and help new members Have fun hacking and learn new stuff! Set up and maintain build tools and test automation	Misa is our new lab member and helping me to write the program to convert the mapping format to the sam format. I hope he can help me more.
lijua...@gmail.com	Contributor	Develop tools for downstream analysis Document our development process and help new members Lead by providing a project vision and roadmap Test the system before each release	Dr. Lijuan Mo was the senior student in Prof Chen's lab and is a postdoc testing my program. I sincerely appreciate her help.

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