His groups built a biorepository inventory management software, community portal software, bioinformatic analysis tools (often web-based).
- Martin Fenner
need to get lots of citations of tools to keep getting funding
- Cameron Neylon
Individual tools are not in a vacuum, they should be connected together as cyperinfrastructure.
- Martin Fenner
lots of web based tools but individual tools are not in a vacuum. The collection of resources is key and how to combine them together
- Cameron Neylon
nasa space programme as an analogy for building an integrated cyberinfrastructure
- Cameron Neylon
each part can be tightly specificed for e.g. shuttle but harder to push that kind of integration specification for funded research projects
- Cameron Neylon
Difference in space program: NASA clearly says what they want, different in bioinformatic tools.
- Martin Fenner
Examples of integration (cyberinfrastructure) tools, CaBIG, NCBI, BIRN, homw-grown...
- Martin Fenner
Administrattors always want "big picture", e.g. asset management, researchers want data analysis. This leads to two kinds of projects.
- Martin Fenner
researchers totally focussed on specific problems. Administrators have other concerns, want "asset management"
- Cameron Neylon
administrators often misjudge their needs for scientist's needs. Scientists often mistake today's need for tomorrow's needs
- Cameron Neylon
NIH has 27 institutes, they all have their own approach to informatics.
- Martin Fenner
Traditional approach: domain specific coordination
- Martin Fenner
traditional approach is to build a specific system or portal for a consortium of researchers
- Cameron Neylon
Data sharing was key to PGRN's value - but not the last place the data might go
- Cameron Neylon
horribly complicated workflow with lots of different research foci
- Cameron Neylon
i guess this approach creates isolated domain knowledge that is hard to integrate with other domain specific projects
- Pedro Beltrao
Need to collect disparate data to pull everything together and then push on to the mandated site
- Cameron Neylon
Management needs: secure platform, database eneabled
- Martin Fenner
Question: are researchers actually using the web-based tools to collect data?
- Martin Fenner
and every lab is probably doing something different to the workflow they say they are using...
- Cameron Neylon
but if you designed better to start with (but need heavy resourcing to do this) then it might be
- Cameron Neylon
CaTissue is great tool for tissue sampling, was built from the beginning to work for many different situations.
- Martin Fenner
Current challenges: connect to bigger projects, next generatin suequencing, etc.
- Martin Fenner
pedro asks a good question - is there any mandate for annotation or tagging? Answer from Sean: No, there is money available to support but no compulsion
- Cameron Neylon
Big mover in the next 10 years: funding for translational research centers (CTSA).
- Martin Fenner
mandates for CTSAs to work together but no idea how that is going to happen in practice
- Cameron Neylon
Ask for a laundry list of informatics functionality. Sean "do you know how much this is going to cost" Admin: "No, how much do you need" Sean: "Well all of the money available..."
- Cameron Neylon
ability to embed applications in a virtual machine in the web portal.
- Cameron Neylon
hub doesn't directly integrate scientific data or handle group collaboration
- Cameron Neylon
personal information actually put into their hub implementation by administrative assistants
- Cameron Neylon
integration across CTSA informatics projects is not happening, everyone is trying to do everything themselves
- Cameron Neylon