SciBar Camp: Keynote by Sean Mooney; Biomedical... - SciBarCamp

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

e.g pharmgkb http://www.pharmgkb.org/ and COBRA breast cancer http://www.pharmgkb.org/views... - 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

http://bioportal.bioontology.org/ - 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

Indiana CTSI hub http://www.indianactsi.org/ - Duncan Hull

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

http://laboratree.org/pages... - Pedro Beltrao

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