ISMB 2014: InfrastructureForNewCores

Introduction

This page was created in response to a suggestion made at the 2014 ISMB workshop. One of the discussions there centered around configuring resources for a core facility and the merits of commercial packages. As an extension of this discussion some people suggested that it would be nice to have an idea of what core pieces of infrastructure people had within their cores, and more specifically to be able to make suggestions for which pieces of hardware and software the group would consider to be useful when setting up a new core and some specific suggestions for packages which could fulfil each of these functions.

• Hardware: buy or rent (AWS)?
  • Assume: ~20% usage for own hardware (my own average for the past year)
  • Assume: assume equivalent pricing on S3 vs institutional storage ($0.03/GB/mo).
  • who does the sysadmin stuff for your own hardware
• Software
  • "Pathway Analysis" software. IPA is ~$6,000/year, or ~$20,000/year for concurrent license. Cheaper/free alternatives?
  • "Plasmid drawing / in silico cloning" tools commercial (CLCBio/VectorNTI) or free, open source solutions?
  • "Sample tracking" and LIMS
  • "workflow managers"
• Time tracking: spreadsheet (easy for startup, hard to scale) vs enterprise solution (more cumbersome initially (?), scales better)
• Hire personnel
  • core people vs. embedded bioinformatician
• Interaction with exiting groups
  • other core facilities (functional genomics, mass spec, etc)
  • computational / statistical Biology research groups
• Setting up a culture of collaboration with the wet lab research groups
  • make sure they talk to you before they start the experiment
  • co-authorship vs acknowledgement
• Teaching
  • offering training courses
  • co-supervision of students