This is an excellent resource for researchers who are new to RNA-Seq or need a refresher.

This GitHub Repository contains all of our scripts and pipelines currently under development by the Genome Informatics Facility.

This is the Office of Biotechnology main page. If you are looking for other facilities services you can find it there.

The abalone community encourages all researchers with an interest in abalone or mollusks to join our efforts and become collaborators in an International Abalone Genome Consortium to improve this valuable resource. Updates will be posted on this website, or to keep informed join the mailing list. If you have any questions, feedback or problems please contact us. We will endeavor to respond in a timely manner whenever possible.

This is a comprehensive catalogue of animal genome size data. If you want to determine how big your genome is before you try to sequence it this is where I start looking for that information.

The NCBI common tree taxonomy browser is a great tool for creating a tree that provides a decent idea of how different species are related. By entering genus and species names in the enter name id field, a taxonomic tree can be constructed for the species of interest.

This paper summarizes guidelines to determine whether a contribution by a statistician or in our case bioinformatician is considered significant and warrants authorship.

Internal Dokuwiki for GIF

Grokking GATK: Common Pitfalls with the Genome Analysis Tool Kit (and Picard) Sam Nicholls The Genome Analysis Tool Kit (“the” GATK) is a big part of our pipeline here. Recently I’ve been following the DNASeq Best Practice Pipeline for my limpet sequence data. Here are some of the mistakes I made and how I made them go away.

The High Performance Computing (HPC) Group provides training, assistance, and support for research and high performance computing as well as engaging in funded research projects. Specific areas of expertise include:

Training and assistance for researchers and students in high performance computing (HPC)

Shared and distributed memory parallel programming

Selection and development of efficient algorithms for scientific computing

Program optimization, particularly those using large amounts of data, memory, or CPU time

Porting codes to HPC systems

Support for the high-capacity, high performance computing facilities of the HPC Partnership

Support for HPC facilities for students

The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past 10 years. Here, we discuss commonly used high-throughput sequencing platforms, the growing array of sequencing assays developed around them, as well as the challenges facing current sequencing platforms and their clinical application.

The Iowa State University DNA Facility in Ames Iowa provides Sanger sequencing, genomic or massively parallel DNA sequencing, oligo DNA synthesis and other biotechnology laboratory resource services for researchers in academia, industry, and government.

The Protein Facility of the ISU Office of Biotechnology is open to faculty and students from the university, other educational institutions, and industry scientists. The facility offers protein/peptide sequencing, large and small peptide synthesis (Fmoc), matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, circular dichroism, SDS-PAGE/blotting, 2-D gel electrophoresis, isoelectric focusing (IEF), in-gel digestion/peptide mass fingerprinting, digital image acquisition and analysis using the Typhoon imaging system and the 2D gel documentation/analysis system and preparative, analytical and micro-analytical high performance liquid chromatography (HPLC).

The mission of the W.M. Keck Metabolomics Research Laboratory (MRL) is to provide researchers services that enable the high-throughput chemical analysis of metabolites and metabolism. The MRL is equipped with a variety of state-of-the-art analytical instruments that provide researchers with analytical flexibility to analyze a diverse set of metabolites with a variety of chemical and physical properties. The MRL has the capacity to conduct these types of analyses on a 24-hour a day, 7-days a week basis. The establishment of the MRL was made possible by a grant from the W.M. Keck Foundation.

TimeTree looks for these species in the TTOL to find their most recent common ancestor and produces the time estimate available. All studies with published times of divergence for that evolutionary split are shown in a Table format. When one or both of the species are not present in TTOL, the NCBI taxonomy is scanned to find the closest relatives of the species or higher taxa requested by the user. Then, those taxa are used as proxies and the most recent common ancestor identified to generate the final time estimates.

VIM Adventures is an online game based on VIM's keyboard shortcuts. It's the "Zelda meets text editing" game. This is a great resource for new users of VIM. Learn shortcuts and become proficient at Unix's most powerful text editor. So come have some fun and learn some VIM!