13th Discussion-5 November 2012

Brief Description and Continuing Discussion:

Topic 1: The role of core facilities in an age of embedded bioinformaticians (Led by Matt Eldridge and Hans-Rudolf Hotz)

This topic developed out of the informal bioinfo-core meeting held at ECCB 2012.

Introduction and Preliminary Information

Many research groups now generate sufficient informatics work that they are appointing bioinformaticians directly into their group. Often, these are the only computational positions in an otherwise research-oriented group. This raises some interesting questions about the changing role of the core facility and how 'embedded' bioinformaticians can be supported in their position.

In 2011, Kallioniemi, Wessels and Valencia commented on how bioinformatics core services could be organized in face of this emerging model [Bioinformatics (2011) 27 (10): 1345]. They suggest a changing nature of the core service with an emphasis on more general, institute-wide support activities. Interestingly, they envisage the scenario in which there are many more embedded bioinformaticians within an institute, primarily funded by grant income and engaged in more reseach-oriented work, than institutionally-funded core bioinformaticians. The need to develop structures that allow the embedded bioinformaticians to meet and communicate was highlighted as very important.

The questions for our discussion are:

• To what extent is the embedded-bioinformatician model being adopted?

• Has this model affected the volume and type of support from the core?

• Is there more emphasis on general, institute-wide support activities at the expense of more direct involvement with biologists on specific research projects?

• What impact is this having on the core's ability to retain high-calibre staff and to deliver services, e.g. training, analysis pipeline development, etc., which require staff to stay current with latest experimental techniques and analysis approaches?

• Is there a role for the core facility to play in helping to bring together the bioinformaticians from various research groups, helping to foster interactions and provide a more conducive environment for computational scientists across the organization?

• how to hire an embedded-bioinformatician ? Is the core-facility involved in the selection process?

Topic 2: Challenges and finding in Integrating multiple high-throughput data types (Led by Simon Andrews and David Sexton)

A thorough study of a particular experimental system can now involve the production of multiple high throughput datasets from diverse types of experiment (RNA-Seq, Histone modifications, Methylation, Imaging, Mass Spec). While there are many choices for user-friendly tools to analyze large datasets from a single experiment type, there seems to be very little which would allow you to integrate information from many diverse data sources to be able to make biological conclusions about the system as a whole. How are people handling these types of experiment?

Preliminary Information

Questions which may be relevant to this discussion:

• How are people handling these types of experiment?