Biomedical Informatics Lab (BIL)

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Facilities

Computing Facilities at BIL

Hardware Platforms

Imaging Server:

Sun Fire V40z Server consisting of 4 CPU 2.6Ghz single core processors, 32 GB RAM and 10.8 TB of storage for external user. This server is targeted for supporting complex massive image processing and storage, such as microscopic images. The server is supported by a Sun Fire V4200 family Server consisting of 2.6Ghz single core processors, 1 GB RAM and 3.15 TB external storage is connected to imaging server to serve as bioinformatics database server. This complements the imaging server to store and manipulate genomic and proteomic data. It mainly comprises of DB2 and MySQL. Imaging and database server supports research projects associated with SMA Computation and Systems Biology (CSB) program.

 
Bio-Grid
All the servers in BIL are connected in a grid architecture in order to maximize the utilization of the computing power and storage of all servers, using middleware Globus 4.2.
 

 

​Software
Bioconductor: bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
Blast: basic local alignment search tool
Autodock: suite of automated docking tools that is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure
Bioperl: collection of perl modules that facilitate the development of perl scripts for bioinformatics applications
BlastZ: independent implementation of the gapped blast algorithm specifically designed for aligning two long genomic sequences
Definiens: The Definiens Enterprise Image IntelligenceSuite is a comprehensive image analysis platform for two-dimensional (2D) image analysis. It contains all the client and server software needed to extract intelligence from any digital image in a fully-automated or semi-automated way. The client software is role-based and supports the needs and skills of different users in an organization. The server software, known as the Definiens eCognition® Server, is a processing environment that allows the batch processing of jobs. It is hugely scaleable, capable of handling millions of images in a single job.
Ensembl: freely available software system for genomic analysis that cope well with rough draft data
Gromacs: open-source molecular dynamics package
Imaris: Imaris is Biplane’s core software module that delivers all the necessary functionality for visualization, segmentation and interpretation of 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size. Conveniently load, process and visualize images acquired from almost any confocal and wide field microscope to gain new and groundbreaking insight from your image data.
Matlab: tool for doing numerical computations with matrices and vectors
MySQL: open-source database
pgSQL: open-source database
R: R is a open source software for statistical computing and graphics
S-Plus/Insightful Miner: statistics software and data mining software