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.