MCIC Computational Biology Laboratory (MCBL)
Our mission is to build core support and intellectual leadership in the area of bioinformatics to support research at the OARDC, by providing an engaging work environment, space, infrastructure and training for performing research involving biological data analysis. We aspire for the MCBL to become the place to be for learning and performing bioinformatics research at the OARDC, the place where ideas are discussed and exchanged, students and users learn from each other and get help and support from our experience staff when needed, and we as a community move our bioinformatics knowledge forward.
Become MCIC Computational Biology member (MCBL) member by completing this on-line registration form.
MCBL Registration
| What we provide | |
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Dedicated computer laboratory, restricted to MCBL members, with eight workstations connected to a server that has been pre-installed with software, algorithms and custom scripts for sequence data analyses. |
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Customized version of Galaxy server (http://galaxy.oardc.ohio-state.edu) |
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If more than one laboratory is interested in commercial software, we will host the software on our workstations. |
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Two dedicated workstation for memory intensive processes (such as assemblies and genome/transcriptome annotations). |
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Custom analytical workflows for data analyses. |
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Staff available for consultation and to provide assistance for genetic data analysis, statistics and trouble shooting. |
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Free access to training and workshop sessions organized by the MCBL staff. |
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Access to the MCBL computer laboratory for teaching classes to member laboratories. |
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Digitally expanded lab space to include 24 hour video-linked to Columbus campus with CAPS Computational Biology Lab (CCBL) and accesses to CCBL activities, including seminars, journal clubs and problem solving workshops MCBL governance. |
| Advisory committee | |
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The role of the advisory committee is to assist the MCBL staff by assessing new bioinformatics needs, providing advice on setting priorities, identifying infrastructural needs and recommending policies and procedures for the fair use of the MCBL infrastructure. |
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MCBL members will select 3 to 5 faculty or senior scientists from different MCBL user laboratories, and at least one member from another bioinformatics core laboratory, to serve on the advisory committee. Each committee member will serve a year term, renewable for up to two times. |
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Committee meetings will be held at least semiannually or when needs arise. The committee will review the progress of MCBL activities during these meetings. |
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MCBL members and the advisory committee will review and evaluate the progress of MCBL and provide feedback to the MCIC Head. |
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Revise and update the current mission and governance of the core. |
Become MCIC Computational Biology member (MCBL) member by completing this on-line registration form.
MCBL Registration
Upcoming tutorials
Introduction to R-Studio and R: This is an introduction to R software for beginners. The workshop will include three sessions: (1) an introductions to R basic tools, (2) graphics and data visualization in R, and (3) how to perform basic statistical operations in R. This tutorial is planned for Spring break week, March 12 and 13. You can find details about the topics that will be covered in this document [PDF]. Please contact Stephen via e-mail (opiyo.1@osu.edu), if you would like to reserve a spot or get more information regarding this upcoming workshop.
RNA-Seq and transcritome assemblies: Asela is planning to repeat the RNA-Seq tutorial in December and will be sending out more information regarding the dates shortly. However, if you are interested in participating, please contact Asela via e-mail (wijeratne.1@osu.edu) so that he can reserve a spot, as last time we had more requests that we could accommodate. A detailed description of the topics covered can be downloaded here [PDF]. You can help us improve the workshop and update the topics, by providing us feedback by taking this short survey: http://www.surveymonkey.com/s/K7RKGSY.
Software listed below is avilable as standalon, or most of these packages have been integrated into the the customized MCIC Galaxy
site.
De novo assembly software
• Velvet (genome)
• Rnnotator and Trinity pipelines (transcriptome)
Guided assembly
• Mosaik (genome)
• Tophat, cufflink and cuffmerge (RNAseq)
Read mapping and search algorithms
• Bowtie (short read mapping)
• BWA (short read mapping)
• GMAP (est mapping)
• Blast
• Blat
• Tophat (short read mapping)
• Lastz for 454 reads
• Mosaik aligner (Indel and SNP)
Sequence data quality control
• FASTXtoolkit (various manipulations of fastq and fasta files)
• FastQC (initial quality assessment of short reads)
• Cutadapt (removal of adapter sequences)
• Custom perl and python scripts from UC Davis Genome Center for quality trimming o RNAseq
• DESeq (differential gene expression)
• EdgeR (differential gene expression)
• Cuffcompare and cuffdiff (differential gene expression)
• Blast2Go (automated annotation pipeline; runs on a local machine with local databases (nr, refseq, custom databases) to improve speed and to handle large number of sequences (~50,000)
SNP and indel analyses
• SAM tools (SNP calling from HT data)
• Indel Analysis
Custom algorithms for quality checking of de novo RNAseq assembly
• Fasta file manipulation tools (e.g., fasta header formatter)
• Genome file manipulation (e.g., extract genome region from a fasta file given a genomic region)
• Text manipulation tools (e.g., cut a column)
Tools that on local computers
• Blast2Go (automated annotation pipeline; runs on a local machine with local databases (nr, refseq, custom databases) to improve speed and to handle large number of sequences (~50,000)
• Automated RNAseq workflow that runs using a bash scrip to handle a large number of samples in cases where it is too time consuming to upload into Galaxy (there will be more workflows available in near future for small RNA and SNP analyses).
• Python script to paralyze blast searches for a large number of sequences
• IGV browser for visualization
• Other custom scripts made by MCBLstaff