The Arkansas INBRE Core thanks to grants from NCRR (P20RR016460) and NIGMS (P20 GM103429) at NIH) partially underwrites the MidSouth Bioinformatics Center (MBC) at UALR. The MidSouth Bioinformatics Center (MBC) provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure to aid faculty, students, and researchers in the region with their bioscience computational needs. In addition to private one-on-one sessions, the MidSouth Bioinformatics Centers offers workshops, training on specialty topics, and computing resources including software, computing cluster, and technical advice.
Arkansas INBRE dollars in combination with funding from UALR and other sources cover the expenses associated with employing a full-time Technical Director, graduate assistants, and the purchase and maintenance of the necessary hardware equipment and software licenses. The MBC has assembled a variety of computing platforms that allow bioinformaticians to store and analyze life science data. The Bioinformatics Core is strongly committed to the use and promotion of open-source software. Most of the software supported by the MBC is either open-source or developed in-house. A brief listing of tools packages and applications is listed here.
- Programming languages – R, Perl, Python, C/C++
- Tools for next-gen data – tuxedo package (tophat2, bowtie2, cufflinks, cummeRbund), trimgalor, trinity, FastQC, Genome Analysis Tool Kit (GATK), bismark, fastx toolkit
- Miscellaneous packages – EMBOSS, ViennaRNA package, samtools, tools from NCBI (ncbi-blast, sratoolkit), tools from Novocraft, hmmer
- Machine learning – C5.0, Cubist
The core of the computational infrastructure at the MBC is a new large storage fileserver. We use a system integration approach to make the data available to the rest of the infrastructure through a private network switch. This includes a small High-performance Computing (HPC) cluster (Rocks OS) and a distributed-memory multiprocessor system with message-passing (MPI) for running independent jobs simultaneously. This cluster is used as a teaching tool. For example, it can be used to compare and contrast the shared memory systems with distributed memory systems. Students have the opportunity to write and test code on the MBC’s cluster and thus become familiar with submitting jobs using schedulers on the Center’s cluster, which helps them to understand and apply their skills to larger more powerful institutional clusters like the UALR High Performance Computing systems.
The target audience for our systems includes all researchers who are working with “omics” data. The MBC can store and process large data sets (i.e., in the form of next-generation *.bam, *.sam and *.fastq files, as well as other formats). The MBC has set up a new fileserver with 22TB of storage and 128GB of RAM. One of its roles is as a file server for both the MBC’s shared memory systems and cluster. The new MBC server with 128GB of RAM, along with a machine that has 64GB RAM, is used for RAM-intensive jobs. For CPU-intensive processing, the MBC has several multi-CPU systems including the new server with 16 CPUs, and two servers with 16 and 8 CPUs, respectively.
For more details on the MidSouth Bioinformatics Center, please contact us today:
Dr. Phil Williams
MidSouth Bioinformatics Center
University of Arkansas at Little Rock
EIT Building, Room 326
2801 South University Avenue
Little Rock, Arkansas 72204