wiki:Bioinformatics

Notes with Gerry Lushington and Joan Hunt June 22, 2010 (Russ Waitman, scribe)

IAMI - a strength, mention favorably.

Telemedicine has been a great model for Joan and the KINBRE teleresearch network. Check with Ryan and David about how much or if the telemedi

CaBIG GSK -- need to equate the two.

Aim 3: the cancer center initiative has many of the pieces we need for the CTSA

  • the funding is minimal though right now as the initial funding is from the State. So, the facilities are not as solid
  • the ideas are good
  • Deliver the same support for other projects to the CTSA, will require the same general support

Non-cancer research support as a focus for CTSA? , diabetes, spine, reproductive

roughly 50-50 right now for Cancer between Gerry and IAMI.

Support…. what is there? KUCC pilot award Most of IAMI work is fee for service but coming from internal sources.

  • Scott gets money from the state, then goes to Gerry as fee for service.

Gerry to need money for oversight

  • but, needs infrastructure for data management. Long term maintenance issues and customizations. "A core" expense.

Hardware and software?

Curation and storage of data.

Joan: too many bioinformatics arconyms in our section.

What do the researchers need?

  • need the annotations and the molecular integrated?
  • who can confirm this for us? Osama Tawfik. a Bansal at the VA.

tissue -> path report (clinical annotations also in the overall chart) -> bioinformatics analysis -> raw signals -> summarized molecular signatures.

  • utilization of the data may be at the discretion of the initial investigator.

Gerry: target clinicians who have an interest in molecular profiling and interrogation.

There is imperfect data flow with the clinician works with a basic biologist.

this is basically a personalized medicine type problem but with the research team doing the molecular diagnostics.

Joan: a couple key people we could ask about their needs from the T1 bioinformatics needs. KINBRE: Partnerships for translational research training

  • Mark Cohen, MD, Laird Forrest on Lawrence campus: evaluating lymphatic targeting of cisplatin fibroid cancers
  • Sam Kim MD in OBGyn and David Albertini in reproduction - cell cycle regulation in oocystes.
  • Inhibition of a protein in Cancer, Karen Kelly.

Support for drug discovery:

  • models right now are highly generalized. They are giving feedback to basic scientist on cell line screens.
  • then go to animal model
  • then go to phase 1 clinical trial.

Joan: Guidance for how we will facilitate researchers clinical and basic to partner and approach problems

  • great example that is advanced is Lisa Harlan Williams BRCA1 expression.
  • chemical biology screening data - goes to chemist for lead optimization strategies
  • in parallel in silco prediction for distribution and toxicity.
  • Also, Curt Klassen

Joan: need clear illustration of the goal. Example, bolded summaries in places. Clear outline of the paragraphs.

Data storage? Gerry ok right now for things except high bandwidth imaging results. 30TB in their current environment.

  • may want to state storage capabilities for Bioinformatics storage.
  • understand the university G drive.

Joan can share the bioinformatics core for KINBRE

  • how do collaborate
  • how do we set priorities
  • who has the final say

We are WORKING TOWARDS the linkage of clinical and bioinformatics results.

Russ to do: meet with

  • Curt Klaasen - drug discovery - high throughput screening applied to cell lines
  • L Harlan Williams - biochemist located in cancer center space. drug discovery - high throughput screening applied to cell.
  • Osama - biomarker

If we fully utilize the KINBRE we could also show how we have expertise from the other places at the state. KSU. Mention how the studios can pull in the KINBRE network for studios.

Gerry offers periodic symposia. Basics of micro array. Does workshops. Also does GRA workshops. Currently sponsored under KINBRE, translational researchers just need to know they can join in.

  • Stimulus grant G20 did get funded. It was to create a data center 6.7 million. Call it the BCLSL. Refers to the machine room and the core group of investigators. Was EECS and KUCR (Kansas University Center for Research).

Joan:

  • double check on if their are exclusions for tables - double check with the program officer.
  • may not be a TRIO, because the work TODAY, that nursing informatics contributes, isn't that big as a bird in hand today.
  • refer to names in parentheses

Stays the same FTE as before for bioinformatics? Take Gerry up in percentage for the first years? 20% minimum. 50% for Mahesh. Anyone else, 100% really a gift from KINBRE to CTSA for a great person.

Joan: need an appearance of a portal before the grant goes in. Need the web page already here for the grant.

Jian Wen Fang at Lawrence helps coordinate informatics at KU.

  • need to be on the same page as the Lawrence campus.
  • KUCR Steve Warren established coordinated informatics
  • he doesn't have a primary academic appointment.
Last modified 7 years ago Last modified on 06/30/10 10:24:24