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Martin Fenner
SciBar Camp: Keynote by Sean Mooney; Biomedical Research in the Age of Cyberinfrastructure
Keynote at an unconference is difficult, an untalk? Will take about why he thinks scientists don't use the internet. - Martin Fenner
hi martin :) - Pedro Beltrao
Is all the discussion on Twitter? - Martin Fenner
seems to be quite a lot over there at #scbPA but we know where the quality is... - Cameron Neylon
Scientists are certainly all connected: email, manuscripts and news on the internet - Martin Fenner
but integration a problem, dissemination of data is a challenge - Cameron Neylon
Most of the tools that his group builds are web-based - Martin Fenner
For the majority of scientists, there is no interest in using tools like Twitter or Facebook. - Martin Fenner
streaming video at http://bit.ly/uTeV4 - not from me at the moment - Cameron Neylon
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
talking about different big programs like https://cabig.nci.nih.gov/ and http://www.nbirn.net/ - Pedro Beltrao
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
the informatician is a sad clown - Duncan Hull
scientists mistake todays needs for tomorrows neeeds - Duncan Hull
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
NIH puts out RFA request for applications - Duncan Hull
data sharing is one of the key values of big collaborative projects like PGRN but details are horrific, complex workflows - Duncan Hull
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
This is just like being at ISMB :-) - Duncan Hull
Question: are researchers actually using the web-based tools to collect data? - Martin Fenner
every lab does things differently - Duncan Hull
a successful workflow in one lab is disastrous in another - Duncan Hull
and every lab is probably doing something different to the workflow they say they are using... - Cameron Neylon
Tools are too specific, don't generalise - Duncan Hull
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
technology moves faster than scientists do, things become obsolete very quickly, e.g. sequencing - Duncan Hull
Current challenges: connect to bigger projects, next generatin suequencing, etc. - Martin Fenner
e.g. national center for biomedical computing http://www.ncbcs.org - Duncan Hull
Mark Musen has one, Russ Altman has another - Duncan Hull
NCBIO Bioportal - Duncan Hull
3 simple tools, integrated ontologies, automated annotation and links to resources - Duncan Hull
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
BIRN biomedical informatics research network http://www.nbirn.net/ - Duncan Hull
Clinical and Translational Sciences Award Informatics will be big - Duncan Hull
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
Administrators bite off more than they can chew - Duncan Hull
Purdue has nice web based collaboration plaforms called hubs, e.g. http://nanohub.org/ - Duncan Hull
More than 70,000 users, people actually use it! - Duncan Hull
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
All PHP and CMS - Duncan Hull
ability to embed applications in a virtual machine in the web portal. - Cameron Neylon
People rarely find each other through social networks, they just use it to spy on their rivals - Duncan Hull
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
scilink, laboratree, labmeeting, researchgate, biomedexperts, scivee, nature network, openwetware - Duncan Hull
And now, the Web2 bit! - Cameron Neylon
lots of web 2.0, hugely popular (really?) - Duncan Hull
this area is of very high interest to the NIH, how do you discover resources that are available to you? - Duncan Hull
popular with adminstrators and funders I think - possibly developers, less so with scientists... - Cameron Neylon
NIH has started to put more grant money into social networking tools, e.g. with the CTSAs mentioned above. - Martin Fenner
don't focus on communities, focus on projects - Duncan Hull
e.g. confluence, sharepoint are extensible tools - Duncan Hull
microsoft booo! - Duncan Hull
but sharepoint very popular in government - never really understood why I have to admit - Cameron Neylon
uses OpenSocial - Duncan Hull
first use case: creation of collaborative documents - Duncan Hull
Challenges faced in Mooney lab: Creation of collaborative documents: manuscripts, proposals, management of datasets, discussion. - Martin Fenner
1200 users for laboratree.org - Duncan Hull
Laboratre solves problems in Mooney lab. - Martin Fenner
Applications can be embedded in Laboratree using OpenSocial. - Martin Fenner
Lessons #1 web portals are under used - Duncan Hull
Web portals for science suffer from under-use. - Martin Fenner
Lessons #2 Killer app is "have to use" not "like to use" - Duncan Hull
Successful tools are simple. - Martin Fenner
Start with an existing community. - Martin Fenner
Lessons #3 "if you build it they won't come" so start with an existing community - Duncan Hull
Discussion: Open Science is important, but is a long way to go (publishing as example). - Martin Fenner
Discussion: will HTML be used instead of .pdf or .doc? Is a paradigm shift, particular difficult in clinical medicine. - Martin Fenner
One reason to use OpenSocial for Laboratree is the hope that people would build applications that can easily be reused. - Martin Fenner
Discussion: a lot of our data from a years ago is probably no longer relevant to what we do today. - Martin Fenner
Darn, would have loved to be at this session. Some day I will actually make it to one of these - Deepak Singh
I posted the keynote as a video in three parts on my blog: http://bit.ly/2G0DE - Naomi Most
Thanks Martin, Pedro, Cameron, Duncan, and Naomi! With so many notes and videos, it is almost like being there :) - Mike Chelen