Bioinformatics

Core Resources
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Core Resources

Bioinformatics Best Practices

We encourage investigators to contact us before starting a project that may require analysis bioinformatics services. This will allow us to have a better understanding of your computational needs, to provide feedback on experiment design (e.g., number of samples, required sequencing depth, appropriate sequencing platform,) and to ensure that the necessary hardware and software resources are in place for timely analysis of the data. We provide free consultation for this purpose. 

Most of our work is performed on HiPerGator, UF’s supercomputer, using open-source bioinformatics software. We also have access to commercial packages such as Ingenuity Pathway Analysis (IPA) and Partek Flow (thanks to support from the UFHCC).

Policies

To access our services, please create a submission in CrossLab, indicating it is for the Bioinformatics Core and including a brief description of your project. We will then contact you for a (free) initial consultation to discuss the analysis details. If your data were generated at ICBR (for example in the NGS Core) you will not need to create a new project, the existing one will be shared with us.

Our services are billed at a fixed hourly rate. We only charge for the time we actually spend working on your data, not for computer time or for storage of your data for the duration of the analysis.  If necessary, we provide assistance on storing your datasets and submitting them to public databases.

Before starting a project, we will provide you with an overview of the analysis appropriate for your experiment type, along with an initial estimate of the number of hours it will require. When the analysis is complete, we will meet to discuss the results and, if necessary, plan downstream (extended) analysis which may involve exploratory work, literature searches and development of new methods and/or software tools. For example, in the case of RNASeq, the basic analysis pipeline goes from initial cleanup and quality control of the input data to generating lists of differentially expressed genes. Extended analysis may include pathway analysis, alternative splicing analysis, clustering, etc.

In addition to the fee-for-service option, we offer long-term bioinformatics support for projects that require computational over extended periods of time.  Under this model, the investigator agrees to pay a fixed number of hours per week and receives guaranteed, continued and consistent support from a member of our team. The number of hours can be changed according to the needs of the project and the agreement can be terminated at any time. We believe that becoming involved in your projects – not just as service providers but as scientific collaborators, thus gaining a deeper understanding of your scientific goals and questions – enables us to provide better and more cost-effective services to our customers.

Acknowledging Bioinformatics

Authorship credit should be given if members of the UF/ICBR Bioinformatics staff have provided services or expertise that is critical to a manuscript. Although other circumstances may warrant authorship, authors are those that meet the criteria below:

  • Agrees to be accountable for accuracy and/or integrity of the work and expertise. In all our work, the person executing the work takes the fullest degree of responsibility for accuracy and integrity.
  • Provides substantial contributions to the experimental design, acquisition and analysis/interpretation of the work.
  • Provides input on drafting of the work (often figures) and approves of the work to be submitted/published. If a member of the facility has made substantial contributions it is expected that s/he will be given the opportunity to review drafts of manuscripts for accuracy/fidelity and should indicate agreement before a draft is moved forward to publication.

If a member of UF/ICBR Bioinformatics has contributed work to a manuscript, but does not meet the criteria for authorship, the corresponding author should acknowledge the UF/ICBR Bioinformatics staff member who provided the data and their contributions should be specified.

These authorship expectations were developed in accordance with several other documents that outline criteria for authorship and can be viewed at the links below:

https://oir.nih.gov/sites/default/files/uploads/sourcebook/documents/ethical_conduct/guidelines-conduct_research.pdf

http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html

Grant Proposal Support

The Bioinformatics Core offers support for the preparation of grant proposals that involve a computational / data analysis component.  We can help generate preliminary data, develop analysis strategies, identify software and hardware requirements and write the relevant proposal sections. We also provide the appropriate Resources and Equipment pages.  This service is free provided that, in case the grant is funded, the related work will be performed by our core.

Please note that although BI core members cannot receive salary support from grants, they can be included in proposals as named investigators, and can provide biosketches documenting their expertise.