The UNL Bioinformatics Core Research Facility (BCRF) is located in the Beadle Center at the east side of the City Campus. The Core offers education, analysis, and computational services in the area of bioinformatics and computational biology.

We provide various standard bioinformatics services (listed under Service Fees) with a quick turnaround time and very reasonable fees.

Besides the listed services for fees, we also:

  • Help with preparing for and writing of grant proposals that include life sciences related computation or analyses. Free if the BCRF is included in the grant.
  • Collaborate on larger projects and grants (please talk to us first to request a quote)
  • Custom-program solutions (Java, Perl, VBA) for something simple as conversion or integration of data files, or on the other end of the spectrum develop and program solutions for large-scale analyses (billed per hour)
  • Give lectures in bioinformatics topics
  • Install and maintain, in collaboration with the Holland Computing Center, up to date software and databases in the Life Sciences (specifically bioinformatics) domain.
  • Provide support for bioinformatics software & analyses on the Holland Computing Cluster. This support is free for up to 3 hours per year per faculty.
  • Host (web) servers and research database-drives web sites (e.g. species specific genome browsers).

Service Fees

Standard Bioinformatics Services (+ denotes minimum cost)

Qa and filtering on next-gen sequencing sample $46 $70 $140
Differential gene expression analysis (microarray) 1) $46 $70 $140
Differential gene expression analysis (next-gen sequences) per comparison 1) $155 $230 $465
Go term enrichment analysis (per list) 1) $40 $60 $120
Ortholog/homolog detection (between two species) $81 $122 $245
Metagenomic analysis (per sample) $81 + $122 + $245 +
Phylogenetic analysis $81 + $122 + $245 +
Transcriptome assembly (de-novo or guided) $278 + $417 + $835 +
Bacterial genome assembly (de-novo or guided) $155 + $233 + $465 +
Viral/bacteriophage genome assembly (pure sample) $115 + $173 + $345 +
Viral/bacteriophage genome assembly (contaminated or sample includes host) $278 + $417 + $835 +
Archae genome assembly (de-novo or guided) $237 + $356 + $710 +
Eukaryotic genome assembly (de-novo or guided) $949 + $1,425 + $2,850 +
Data deposition of microarray, next-gen, transcriptomes or genomes (per deposition) to public database $196 $294 $560
Publication-ready graph of any of the above analyses $40 $60 $120
1) Per analysis (not per sample) additional cost for sparsely annotated species $200 $300 $600

Custom Bioinformatics Services

Please note that for longer analyses (longer than 10 hours labor) it is more cost-effective for the researcher to pay part of the salary and benefits of the Core's staff. The minimum percentage is 2% fte, approximately a week (5 business days) of a staff's work, and increments by 2%. Note that if payment is made for 2% fte, but staff was able to finish analysis in 3 business days, no refunds are given but the remainder is available to you for further analysis within the same fiscal year.
Custom programming/analysis (less than 10 hours) $40 / h $70 / h $140 / h
Custom analysis (more than 10 hours) Ask for quote
System administration per hosted server or storage cabinet (per year) $500 N/A N/A

Additional costs for projects spanning more than 3 months or that require more than 200GB storage:

Permanent storage on raid6 at 1tb / year $1,500 $2,250 $4,500
Permanent storage on raid6 per gb/month $0.20 $0.30 $0.60
Optional (in addition to above):
Weekly backup to tape 1 tb / year $500 $750 $1500
Weekly backup to tape 1 tb / year
(includes off-site storage)
$1000 $1500 $3000

Instruments & Facilities

The Bioinformatics Core Research Facility houses a high performance Linux compute cluster dedicated to Life Sciences research. In total, the compute cluster has approximately 250 CPU cores, 600GB of RAM, and 75TB of central SAS RAID 6 disk storage.

Most of our cluster nodes have at least 8GB of RAM and are available via the Sun Grid Engine job scheduling system and are capable of running MPI jobs.

We have a dedicated 4 CPU 6-core large memory server (320 GB RAM) suitable for larger transcriptome and genome assembly jobs. Two web servers and database backend machines are hosting several UNL database-driven research web sites.

Our main login machine is, which is accessible via ssh, and requires a valid Linux account. Linux accounts can be requested and will normally be activated within two business days.


Jean-Jack M. Riethoven (Director)
Phone: +1 402-472-7949
Fax: +1 402-472-3139
Email Jean-Jack

Fangrui Ma (Senior Bioinformatician)
Phone: +1 402-472-1795
Fax: +1 402-472-3139
Email Fangrui

Stephanie Canny (Bioinformatician)
Phone: +1 402-472-6052
Email Stephanie

Seong-il Eyun (Bioinformatician)
Phone: +1 402-472-1572
Email Seong-il

Advisory Committee

The Bioinformatics Core advisory committee consists of the following tenured faculty:

Zoya Avramova, Ph.D.
Phone: (402) 472-3993
Visit Faculty Webpage

Istvan (Steve) Ladunga, Ph.D.
Phone: (402) 472-6074
Visit Faculty Webpage

Jay Reddy, PhD
Phone: (402) 472-8541
Visit Faculty Webpage

Contact the Core Staff

For technical help with bioinformatics software and databases, and analyses using them on the Holland Computing Cluster, we are glad to help out for up to 3 hours gratis per year per faculty. Please use the email listed below to initiate such help; one of us will contact you within a business day. For larger or scientific help, or to initiate discussion on projects, please contact the Director directly instead.

Email Bioinformatics Technical Support

Contact the Director

Jean-Jack M. Riethoven
Phone: +1 402-472-7949
Fax: +1 402-472-3139

Email Jean-Jack