Center for Proteomics and Bioinformatics

Bioinformatics Division

To make an appointment
Please download and fill out our "Consulting Request Form" (fillable)
and email it back to us (an internal link is provided).

To meet us
The Core is currently located in the Biostatistics Core Facility of
the Case Comprehensive Cancer Center,
Biomedical Research Building, Room G19
(right next to the security office).

For further information about our services, please read below.

Mission of the Bioinformatics Core Facility

The mission of the Bioinformatics Core Facility is to support the continuing research and education mission of the School of Medicine, as well as other core facilities within the School of Medicine and the Comprehensive Cancer Center at CASE. The Core acts as a shared resource for the benefit of the medical, biomedical and research communities. It is aimed at supporting analyses specialized in Biostatistics and Bioinformatics as applied to clinical, biomedical, biological, and environmental projects. Services to investigators come in the form of consultation or collaboration. In a typical year, the core expects to provide more than 1,000 consultant-hours of service.

Who can use the Core services and who are your consultants?

The services of the Core are available to all faculty, staff, residents, fellows, post-doc and graduate students of the university, Case Comprehensive Cancer Center, University Hospitals, and CCF. Consultants are from the faculty of the Division of Biostatistics of the Department Epidemiology and Biostatistics. For your information, the primary faculty of this division and their research specialties are listed here. Case Comprehensive Cancer Center (Case CCC) members may also receive general biostatistics support from the Biostatistics Core of the Case Comprehensive Cancer Center.

How can your research benefit from our involvement?

Protocol of support

Before consulting. Obtaining advice early in a project can often greatly improve the chances of the study, successfully meeting its objectives. Nothing is more frustrating than learning after the fact that your data are inadequate for valid statistical inference, or that your time and resources were wasted by gathering more data than necessary. We strongly recommend that you seek our advice during the design phase of your research, on experimental design and sample-survey planning before gathering your data. Individuals interested in initiating a consultation are requested to download and fill out our simple "Consulting Request Form" (fillable), and then set up an initial meeting with the Core. For resident/fellow/student projects, the faculty mentor is also encouraged to attend this initial meeting.

What should I bring to the first meeting? This form will help us understand and identify among other things (i) the PI or the Requester of the service; (ii) a brief description of the context and the purpose of your project (typically: NIH-style research project title, research program, specific aims, study design; current status; deadlines; source and limitations of funding; intended publication/reprint or document; (iii) and a brief description of your request: type of data, type of tasks to perform, the hypotheses you would like to test and the research questions you would like to answer. It is recommended that this information be prepared carefully to help us review the research needs and further study design issues, estimate the workload, and plan a realistic timetable. Additionally, copies of articles or earlier work on similar topics in your discipline would also be helpful. If you are seeking advice on data analysis or report writing after the fact, then also bring with you a description of the data gathering protocol, and any normalization procedure or transformation applied, etc.... Don't forget the file containing the data and the results of the analysis already performed.

Obtaining consulting. We do not offer walk-in or telephone service. Service is by appointment only (see Johnny). Based on the information you provide, the Core will assign a priority to your project. Typically, you will be contacted within 48 hours. In many cases, a single consulting session is not sufficient. Some projects may continue for days, weeks, or months. If the one hour free consulting session is not sufficient, the consultant will provide a good faith estimate of the time and costs to complete the project and what mechanism of pricing is the most appropriate (as described next). These estimates are not binding.

Pricing and Grant policy

Typically, funding support is required via hourly rates, or arranged as a percent effort of sponsored research. However, support free of charge may apply to your project under strict and restricted conditions as follows:

The initial consulting session (~ of up to one hour) is available at no charge in any case.

Case Comprehensive Cancer Center members. As part of the Case Comprehensive Cancer Center (Case CCC) commitment to its research mission and its partial support of this service, Case CCC members may receive limited support free of charge per project when the latter is identified as being cancer-related and minimal in terms of effort or computational resources. Support for such projects will be reviewed on a case-by-case basis by the Core. In the case of grant proposals, all consulting associated with the grant proposal may also be free of charge as detailed below.

Hourly fees. For projects that do not lead to grant applications and that are well-defined and limited in scope, an hourly charge will be applied. The Core bills for the actual faculty time. The current 2008 hourly rate has been fixed to $50/h. The charging is done by billing a grant or an account through the Department of Epidemiology and Biostatistics. Upon agreement of the present policy, the Principal Investigator (PI) is invited to fill out and sign our "Contract Form" (fillable), where an account number to be charged is to be provided, and where written description of work, time-schedule for completion, and estimated costs agreed upon are specified.

Sponsored Research. Users of the Core who engage in sponsored research are encouraged to include statistical consulting in research proposals. Statistical thinking can contribute greatly to the success of research proposals. At many granting agencies, the quality of statistical planning can tip the balance in favor of funding. If a substantial role for statistics is proposed, we will gladly join in your proposal. All scientific consulting associated with the grant proposal, including assistance in proposal writing, experimental design, sample-survey planning, and subsequent analyses are provided without charge as long as the Core personnel is identified as collaborating investigators and appropriate funding for the Core is included in the grant's budget. This can take the form of a direct-cost line item, or full or partial funding of a faculty member's salary.

Computing Resources

The Bioinformatics Core completed in August 2008 the installation of a High Performance Computing cluster (HPC cluster). The HPC cluster operated by us at CWRU is available for consulting and research purposes. It currently consists of 16 compute nodes (2.4 GHz CPU each) based on 4 Intel Core2 quad processors Q6600 machines each with 8Gb of main memory and 320 Gb Hitachi SCSI hard drive. All nodes run under Centos 5 Linux operating system and are interconnected with Gigabit Ethernet for MPI message passing. The system is easily scalable, and it is anticipated to upgrade the cluster to 64 compute nodes shortly. The HPC cluster can provide high performance computing services to all customers of the Bioinformatics Core. In the case of sponsored research, a user account can be provided with additional system administration services, and database hosting services. The Bioinformatics Core web server is now hosted in the HPC cluster. Please note the change of the URL (http://bioinfo.case.edu/) and update your bookmarks and links accordingly.

Authorship policy

Co-authorship on scientific articles is generally expected on studies where substantive input on design/analysis or computational resources is provided. It is our policy not to forego funding in return for co-authorship.

Acknowledgements

Support is provided by the Dean's Office of the School Of Medicine, the Department of Genetics, the Department of Epidemiology and Biostatistics, and the Case Comprehensive Cancer Center.

Policies may be subject to change. Check our website for updates.

If you need more information, please contact us.