The Molecular Profiling and Computational Biology Core assists researchers in a variety of tasks designing experiments and interpreting results from sequence-based assays, including genome-scale and targeted assays of host (e.g., human) and viral sequences, and the design and interpretation of micro-biome communities. This includes assays such as genome and RNA sequencing, mass spectrometry, and other high throughput technologies.
Investigators at CFAR can partner with Core faculty for appropriate design and analysis of experiments. Access to consulting expertise advanced computational tools and software expertise ensures high-level quality control. The Core will also facilitate access to assay technologies, such as sequencing, arrays, or other high throughput technologies available at any of our institutes associated facilities. All activities—from project-related work to analytical tool development—serve as practical case studies in the Core’s formal training sessions in sequence analysis.
Expertise is provided in the experimental design, analysis, and interpretation of microarray, high-throughput DNA and RNA sequencing, genomics, & proteomics data, and for combining multiple data types together, including with public bioinformatics resources. We can train your staff or conduct these analyses on your behalf.
As new technologies of likely general use are identified this resource works with other center investigators to acquire and deploy those techniques. The tools include computational tools and also their associated laboratory protocols and techniques.
A key aspect of the Core is to provide access to computational tools (some web-based, others standalone) required to interpret sequence data, including phylogenic analysis, classification/clustering, processing RNA- or DNA- sequence data. We spend time to make sure that specialized software is available when needed to the community.
Many researchers need support conducting the laboratory protocols associated with data generation, and our core has wet lab expertise required for every type of assay it analyzes. We can train staff or when the throughput is modest or low, conduct the assays on your behalf with only the need to reimburse costs of materials.
For researchers looking to include HIV sequence analysis in an ongoing or proposed project, we offer support for all aspects of experiment design, data generation, quality control and data analysis, including training staff or conducting analyses on your behalf.
A program that is a variant of the Minimum χ2 (MC) method for limiting dilution assays. It allows the user to specify the probabilities of a false negative and false positive PCR (it is also a tool for the quantitation of ampliable viral templates, i.e., viral load under the conditions of your assay). The program is available either as a java applet that can be run via the web or as a program that can be downloaded and run locally.
The Core resource allows researchers to gain access to specialized expertise that is not ordinarily expected in individual laboratories nor is often accessible through more common shared resources or services. In its most general form all aspects related to the use of any molecular assay that frequently requires non-trivial computational or mathematical expertise; although the services are not limited to the computational component. The core’s expertise includes the laboratory protocols needed to generate the data sets; sequences of DNA or RNA (or RNA subcomponents like polysomes) from host cells (including T Cells) or viruses, and includes both high dimension and also low dimensional assays. We can support consulting, training and technology development and also hands on data analysis or laboratory work when the effort is modest. 1. Short-term and longer term consulting - An email help-desk is staffed for users to submit questions, request meetings to discuss specific analysis strategies, and solicit advice on experiment design and novel research studies. For longer term projects that may not require sustained effort but can benefit from longer term lower level of effort team members can be assigned to assist in supervising your staff who can then implement the plan. 2. Hands on support for laboratory components, data processing and analysis - Staffing is provided for short term projects in the areas of microarray, high-throughput DNA sequencing, genomics, & proteomics data, and for combining data with public bioinformatics resources, including expertise specific to viral sequence analysis (described below), analysis of DNA and RNA sequences of host cells, microbiome, and other assays. We can also provide longer term more intensive support to move a manuscript or specific project past a milestone (like a manuscript acceptance) whenever handing it off is impractical (e.g., whenever the effort at one time depends on understanding of previous steps or decision choices) especially when multiple CFAR investigators are involved. This “hands on” component of the resource is the highest priority of the core. 3. Technology Development and Acquisition -- As new technologies of likely general use are identified this resource works with other center investigators or shared resources to acquire and deploy those techniques, including companion laboratory and computational components; examples include T Cell sequencing, ribosome or polysome profiling, and others. The Core steering committee meets frequently to discuss the potential impact of new technology acquisition. Researchers with ideas should send an email to the helpdesk (CFARcompbio@fredhutch.org) with a description. Whenever new technologies are developed the group begins with a pilot to understand the feasibility and potential expense of providing the service to CFAR. The investigators who are requesting it and will benefit from it are asked to contribute to the pilot, by providing resources such as their own time, or physical materials (specimens) used in the pilot. Pilots are undertaken whenever the steering committee feels that it is worth the price compared to other activities that will be eliminated. 4. Development, maintenance, support and access to software: A key aspect of the Core is to provide access to computational tools (some web-based, others standalone) required to interpret sequence data, including phylogenic analysis, classification/clustering, processing RNA- or DNA- sequence data. A current list of software & some algorithms: http://indra.mullins.microbiol.washington.edu/ https://github.com/fredhutchio/ https://github.com/fredhutchio/argo-navis
To receive services, users should send a brief email to CFARcompbio@fredhutch.org that includes a few sentences describing, briefly, the nature of your questions and your contact information. Core leaders will use this description to assign your request to an appropriate staff member who will contact you for follow-up. Most often you will be contacted by a staff member the same day as the request. Follow-up may include a one-on-one meeting, or possibly email or phone exchanges if that is adequate.