Research Support in Computational Genomics

The US Forest Service (USFS), Siuslaw National Forest, intends to issue a sole source contract to purchase research support in computational genomics, in support of a USDA National Institute for Food and Agriculture (NIFA) and USFS-sponsored research project called the “Douglas-fir Climate Change Transcriptome Observatory (D-fir CCTO). Sole source vendor Peter Dolan Consulting will provide computational and programming support for RNA-Seq data generated on an Illumina Genome Analyzer (GA). The Illumina GA is a new generation high-throughput DNA sequencer that has a limited number of commercial vendors and minimal documentation for sample analysis. The output from one DNA sample is substantial; raw data files exceed 1 Terabyte in size, and processed data exceeds 100 million records. Evaluation of data quality, and development of analytical pipelines for data analysis archiving require knowledge of the specific data output of the Illumina GA, proficiency in bioinformatic programming languages (PERL, PYTHON, C), skill in efficient code development, and expert-level training in statistical and mathematical modeling to evaluate signal and sources of error. The computational support provided by Peter Dolan Consulting will enable the Pacific North West Research Station to evaluate genomic responses of Douglas-fir to changes in seasonal climate, as part of this USDA-NIFA funded grant. In support of the D-fir CCTO project, Dr. Dolan will: (A) Provide computer science programming and mathematical support for setting up a data analysis pipeline for RNA-Seq data. (B) Develop a ‘transcriptome reference library’ from publically available gene sequences from Douglas-fir and related conifers. (C) Lead the analysis of RNA-Seq data from a large number of genomics sequences (42 total). (D) Develop a submission pipeline for public archiving of RNA-Seq data. (E) Provide training and consultation with geneticists at the PNW Research Station to assist in the completion of the D-fir CCTO project. Dr. Dolan is the author of “TileQC”, an open source data manipulation system designed for quality control of Illumina GA data . This program is designed to transform and filter the initial data into a high quality, low error form suitable for subsequent statistical analysis. As author of the software, Dr Dolan is the sole expert in its use and maintenance in the United States, giving him the unique combination of training and experience to adapt the pipeline for analysis of RNA-Seq data produced by the D-fir CCTO. He will play an essential role in the application, expansion, and modification of the software for RNA-Seq applications, and the role of co-investigator on the D-fir CCTO study. To our knowledge, no other individual in the United States has the combination of skills necessary to perform all of these tasks. The U.S. Forest Service, Siuslaw National Forest, intends to issue a firm-fixed price for the services stated. This action is taken pursuant to 41 U.S.C. 253(c) (1) as implemented by FAR 6-302-1, only one responsible source and no other supplies or services will satisfy the agency requirements. The solicitation number assigned to this effort is AG-04T0-S-10-0003 and it will be issued on or about fifteen (15) days after release of this notice. This notice of intent is not a request for competitive proposals, however, all responsible sources may submit a proposal which will be considered by the agency.