The MidSouth Bioinformatics Center at UA Little Rock provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure to aid faculty, students, and researchers in the region. Our aim is to promote bioinformatics and open the door to other data sciences. The Arkansas INBRE Core, thanks to grants from NCRR (P20RR016460) and NIGMS (P20 GM103429) at NIH, partially underwrites the MidSouth Bioinformatics Center (MBC).
In addition to private one-on-one sessions, the MidSouth Bioinformatics Center offers workshops, training on specialty topics, and computing resources including software, computing cluster, and technical advice.
Arkansas INBRE dollars, in combination with funding from UA Little Rock and other sources, covers the costs of employing a full-time technical director, graduate assistants, and the purchase and maintenance of hardware equipment and software licenses. The MBC has a variety of computing platforms that allow bioinformaticians to store and analyze life science data.
Software, Tools, and Applications
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. The tools packages and applications include:
- 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
Bioinformatics data sets are often large and complex, requiring computational resources beyond the typical laptop and desktop computers. At the MBC, we host servers for data science.
The target audience for our systems are researchers working with large data including “omics” file types. The MBC can store and process large data sets. For example, this includes next-generation *.bam, *.sam and *.fastq files, as well as other formats.
We have servers suitable for both RAM and CPU intensive jobs. For CPU-intensive processing, the MBC has several multi-CPU shared memory systems. These include two servers with 128GB of RAM, one with 36 CPU cores, another with 32 cores. Our newest server has 22TB of storage, 192GB of RAM, 48 CPU cores and three Tesla T4 GPUs. This server is used for deep learning and running Alphafold2 protein structure predictions.
Providing Support
The MBC works with students and faculty on their data research in bioinformatics, biology, and related fields. We also work closely with the University of Arkansas for Medical Sciences and Arkansas Children’s Hospital. We are committed to providing support to others in the region.
More Information
If you need support with bioinformatics or have questions, please email us a help request.
For more details on the MidSouth Bioinformatics Center, please contact Dr. Phil Williams at 501-916-5244 or phwilliams@ualr.edu.
Address:
MidSouth Bioinformatics Center
University of Arkansas at Little Rock
EIT Building, Room 326
2801 South University Avenue
Little Rock, Arkansas 72204
