Bioinformatics

This core is a cooperative effort between Alaska EPSCoR and Alaska INBRE and was established largely due to the efforts of Dr. Thomas Marr. It is staffed by three full-time IT specialists.

The overall purpose of the core is to adapt and optimize informatics software to provide data management and analysis for investigators in the Alaska EPSCoR Research Focus Areas of Integrative Approaches to Environmental Physiology and Population Genetics of Adaptation to Arctic Environments, for the Alaska INBRE faculty, and to assist others who have needs in computational biology and bioinformatics.

The bioinformatics group makes use of the Apple Xserve G5 Cluster purchased in Phase I of Alaska EPSCoR, the Alaska Metagenomics Site, as well as the Linux Penguin cluster (funded by Alaska INBRE), which includes a mirror of GenBank from NCBI.

Development of the clusters has included:

a. authored a graphical web services editor and invocation environment ("Portal"), which enables the users to utilize the cluster through web interfaces (released under open-source licence, GNU Public Licence, and widely available to scientific communities);

b. creation of 37 xml descriptions of applications that were incorporated into the "Portal" web interface, five of which were parallel applications requiring custom wrapper code, new applications continuously added;

c. creation of numerous web pages of documentation for all 37 applications;

d. implemention of support structure for community-based, web-based tutorials and tips for biological softwares (under development);

e. authored data conversion utilities for research faculty;

f. implementation of web-based custom analysis pipe-line to automate workflows of individual researchers;

g. continued development of PCBL, released version 1.1c;

h. altered hmml source code to achieve 10-fold speedup with identical results, making large problems tractable;

i. installed and maintained general scientific applications (e.g., R, bioconductor, programming environments);

j. authored scripts to automate cluster backup and weekly data updates;

k. construction and installation of two firewalls, one for the G-5 cluster and one for the bioinformatics office; and

l. authored a custom cluster kit with Darwin OS and Linux OS.

Support and consultations for biological computation are widely available to the research community of Alaska.

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