KIDDRC Request System
Sunday Nov 23, 2014

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Mission and Goal

The Bioinformatics Facility at KUMC serves as a resource for providing expert and timely bioinformatics consulting and data analysis solutions. The Facility offers services to investigators both within and outside KUMC on both grant-funded and chargeback-based projects for management and analysis of large-scale biological datasets produced by high-throughput genomics experiments.
The Bioinformatics Facility’s mission is to provide and maintain an infrastructure for state of art bioinformatics analysis.

The Facility’s primary goal is to identify opportunities and implement solutions for managing, visualizing, analyzing, and interpreting genomic data, including studies of gene expression (RNA-seq and microarrays), pathway analysis, protein-DNA binding (e.g. ChIP-seq), DNA methylation, and DNA variation, using high-throughput platforms in both human and model organisms.

Funding Models

The Bioinformatics Facility is a cost-recovery operation. We will work with the investigator to find a funding model that works best for each individual lab or center/department. Funding options include:

Model 1: Fixed Cost. The Facility offers a fixed-cost option for standard "secondary" analysis. This includes next-generation sequence alignment and transcript assembly, differential gene expression with RNA-seq, and microarrays.

Model 2: Fees For Service. We offer an hourly fee-for-service for all bioinformatics analysis services. This is the preferred model for downstream "tertiary" analysis, custom solution development, and extraction of biological meaning from experimental results, where it is often difficult for both investigators and bioinformaticians to place a fixed time/cost on certain open-ended questions. The Facility places a high value on transparency: we attempt to provide accurate effort forecasting and use a time-tracking platform for effort reporting.

Model 3: Research Collaboration – Bioinformatics Facility Personnel on Grants
• Bioinformatics Facility faculty/staff member is a co-investigator on grants submitted and awarded.
• Bioinformatics Facility personnel % time on a grant should be representative of the actual effort required to meet deliverables. (In no case should effort be less than 5%.)

Model 4: Subsidized Services
• Other KUMC entities (department, division, or center) may subsidize Bioinformatics activities. Members of these entities receive subsidized services in proportion to the contributions. For example, members of the Kansas Intellectual and developmental Disabilities Research Center and the Developmental Biology COBRE are eligible for subsidized services.

Authorship and Attribution

A frequently asked question is whether research methodology consultants should be co-authors on scientific papers. Decisions about authorship should be independent of consideration of funding sources. As recommended in published guidelines (Parker & Berman: Criteria for authorship for statisticians in medical papers. Statistics in Medicine 17: 2289-2299), "The basis of financial support should be the time/effort spent on a project and the basis for authorship should be whether [the consultant] has made a scientific contribution to the project." If appropriate, it is often beneficial to include bioinformaticians as authors in publications since those are considered as the most critical evidence of long-term bioinformatics collaborations in most current grant funding reviews.

By JAMA's criteria for authorship for statistical experts involved in data analysis and interpretation, an analytical consultant is a co-author if (1) he/she took part in the drafting of the manuscript or (2) he/she was involved in a critical revision of the manuscript for important intellectual content.
Above all, it is important for the researcher and Facility personnel working on the project to agree on criteria for authorship early in their collaboration.

In cases where bioinformatics core personal contributed to the intellectual development of the project, provided analysis of the data beyond that which would have been otherwise possible for the investigator’s team, or authored any component of the text, authorship should be provided on the resulting manuscript or abstract.

Examples of scientific contributions are the following.

1.    Facility staff develop new methods to meet the project's needs, or combine existing techniques in a novel way.

2.    Facility staff have a significant role in designing the study.

3.    Facility staff write part of the manuscript other than a standard paragraph or two describing which methods were used.

4.    Facility staff are asked to critique an initial draft and spend a considerable amount of time suggesting alternative wording and presentation of results.

5.    Facility staff provide data analysis along with biological interpretation of results.

Data Handling

All Next Generation Sequencing data will be held in KUMC Facility storage for the duration of active analysis. Thereafter data will be subject to deletion. It is the responsibility of the investigator to ensure that copy of data is preserved for the future analysis.

All microarray data is maintained on MDMS (http://bioinformatics.kumc.edu/mdms). However, it is recommended that investigators maintain copies of the data.

Terms and Conditions

Payment. Client agrees to pay for any services in accordance with the agreement. The bioinformatics Facility requires payment arrangements be made before any services are performed, and for payment to be completed upon results are released. Unless otherwise specified by the KUMC Bioinformatics Facility, all payments are due and payable within thirty (30) days of the date of the invoice. Payment shall be deemed late if not received within such time and shall be subject to interest equal to 2% per month, together with all costs and expenses (including without limitation reasonable attorneys' fees and disbursements and court costs) incurred by the KUMC Bioinformatics Facility in collecting such overdue amounts.

Warranty. The KUMC Bioinformatics Facility agrees to conduct analysis and perform the services agreed upon in accordance with the highest scientific and professional standards. All parties recognize and understand that the Facility provides services to explore an intellectual question or scientific hypothesis. The Bioinformatics Facility makes absolutely no warranties, express or implied, and disclaims all warranties including, but not limited to, implied warranties of merchantability and fitness for a particular purpose. The client's exclusive remedy is, at the KUMC Bioinformatics Facility's sole option, a credit for, or reperformance of, the services in question. In no event will the KUMC Bioinformatics Facility be liable for any consequential, incidental, special or indirect damages, including without limitation, damages for loss of profits, business interruption, loss of business information or property damage sustained by client from the use of, or inability to use, any results, even if the KUMC Bioinformatics Facility has been advised of the possibility of such damages.

Confidentiality. Both parties each agree to maintain in confidence and not disclose to third parties any confidential information that is disclosed to one by the other party. This includes pricing information and all communications.

Data Handling and Intellectual Property. Following settlement of all invoices, all compilations of scientific and technical data produced or prepared by the KUMC Bioinformatics Facility in the performance of services requested shall be the exclusive property of the client and shall be deemed to be works made for hire. Any work resulting from unpaid services and all associated intellectual property shall remain the exclusive property of the KUMC Bioinformatics Facility. By using the KUMC Bioinformatics Facility, unless otherwise specified and agreed upon by both parties, the client gives permission to the KUMC Bioinformatics Facility to utilize his/her data for internal development of Facility services, after services are complete and deliverables are met. These provisions shall survive any termination or expiration of this Agreement.

Bioinformatics Service Request

Principal Investigator Information



Requester Information

 

Cost Recovery Information


Project Information

 
Please check all that apply
Project purpose To support an existing, peer-reviewed, funded project.
  To collect preliminary data for a grant
  Other (please specify below after checking)
 
Data Source Microarray: Affymetrix
  Microarray: Other
  Next-gen sequencing: Illumina
  Next-gen sequencing: Other
  RT-PCR
  Mass spectrometry
  Publicly available data (e.g. dbGaP, GEO, ArrayExpress)
  Other (please specify below after checking)
 
Services needed Gene expression: Microarray
  Gene expression: RNAseq
  MicroRNA analysis
  Protein-DNA binding: ChIPseq
  Protein-DNA binding: ChIP-chip
  DNA variation - GWAS or other arrays
  DNA variation - Sequencing
  DNA variation - Variant annotation
  DNA methylation
  Pathway / functional analysis
  Grant preparation
  Manuscript preparation
  Data management/storage
  Other (please specify below after checking)
 



I have read and understand Bioinformatics service and I agree to the terms & conditions and criteria for co-authorship.
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