Neuroinformatics Projects Attract Attention at the 2007 SfN Meeting

“The field of neuroinformatics has seen a tremendous development of new tools and databases over the last few years,” said Jan Bjaalie, director of the Stockholm-based International Neuroinformatics Coordinating Facility (INCF). “But there is a considerable challenge ahead in terms of dissemination of methods and approaches, providing neuroscience with the best that new technologies can offer.”

As part of efforts to disseminate the latest tools and foster communication between neuroscientists, the INCF staff organized an exhibition booth at the 2007 SfN meeting. The well-trafficked INCF booth attracted many participants to its various hands-on neuroinformatics demonstrations organized by the INCF’s scientific officer Raphael Ritz.

For instance, Doug Bowden, researcher at the University of Washington in Seattle, USA, showed participants various facets of the free, online Macaque Brain Atlas under development for the BrainInfo website. More detailed and interactive than a standard anatomy-only atlas, BrainInfo will contain both structure and function information. Types of neurons, locations of particular neurotransmitters and receptors, and gene expression will all be details stored in the atlas.
“Click on a gyrus and BrainInfo will list all the data that has been mapped into the atlas and that overlaps with that gyrus,” said Bowden, who conceived the idea of the atlas in the mid-1970s when lack of resources for anatomical data posed a hurdle in his electrophysiology studies of the primate brain. Launched online on March 1, 2001, the BrainInfo website now attracts substantial traffic: more than 400 visitors query the site in eight languages and view more than 20,000 pages each day.
Also presenting at the INCF’s SfN booth was Andrew Davison, researcher at Centre Nationale de la Recherche Scientifique in Gif-sur-Yvette, near Paris, France. Davison demonstrated features of the software package PyNN (pronounced “pine”), which allows models to be simulated with different simulation programs without translation. “I wrote the first version of PyNN to simplify the task of communicating between simulation groups,” Davison said.

In addition to helping researchers communicate – such as those collaborating on a single project but using different simulators in their home labs – PyNN also makes it easier for researchers to validate a model by running it on multiple simulators and enables researchers to more quickly convert a model to run on their tried and true preferred simulator.

At the INCF booth, Davison attracted visitors who are involved in simulator development and who wanted to better understand how the program could interact with their preferred simulators. “PyNN is the first and so far the only piece of software – as far as I am aware – to provide a common programming interface to multiple simulators,” Davison said.

Another resource for collaborating neuroscientists is the US $9M CARMEN project, which was also demonstrated at the INCF’s SfN booth. Funded by the UK Engineering and Physical Sciences Research Council, CARMEN is developing a virtual laboratory for neuroscientists studying the electrical signaling activity of neurons, helping a diverse, distributed community to share data, software code and expertise. Around 40 scientists at 11 UK universities are engaged in CARMEN's development and prototypical use.

"Our current activities are requirements engineering, familiarizing our user base with technologies that the system will support - such as web services - and rolling out early stage components for preliminary user evaluation," said Alastair Knowles, CARMEN project manager at Newcastle University. At SfN, CARMEN was demonstrated to around 100 visitors at the INCF booth. "The demo generated excitement and a number of unexpected networking opportunities. We are still receiving regular email subscriptions following launch of our mailing list at SfN,” Knowles said in early January 2008.

“Our current activities are requirements engineering, familiarizing our user base with technologies that the system will support – such as web services – and rolling out early stage components for preliminary user evaluation,” said Alastair Knowles, a CARMEN project manager at Newcastle University. At SfN, Knowles demonstrated the CARMEN prototype system to nearly 100 people who visited the INCF booth. “The demo generated unexpected networking opportunities and we are still receiving regular mailing list subscriptions following launch of this feature at the meeting,” Knowles said in early January 2008.

The 100-some visitors to the INCF booth included other neuroinformatics groups. “Having other groups coming to our booth to present computer demos was a great way of making our booth interesting for others, as well as for ourselves,” said Pontus Holm, INCF program officer who joined the INCF Secretariat in August, 2007. “There were always people and something happening at our booth,” Holm added.

In order to better address researchers’ needs, Ylva Lillberg, usability and requirements analyst at the INCF since April 2007, collected feedback from about 20 neuroscientists who visited the booth. She learned that the surveyed neuroscientists find and use software from a variety of sources, including recommendations, papers and conferences, and links from NCBI sites. “Once new software is found, people often find it hard to start using a piece of software that someone else had developed,” said Lillberg, explaining how people often find it too slow and difficult to use new software and they do not feel confident that the data is updated and complete. The INCF’s upcoming software center, which will be released this year, aims to facilitate both the search for software and the development of software.

Other INCF secretariat staff members who attended the SfN meeting were INCF director Jan Bjaalie and INCF scientific information and public relations officer, Elli Chatzopoulou.

Future activities coordinated by the INCF include an exhibit booth and a Neuroinformatics Special Interest social event at this year’s FENS Forum, July 12-16 in Geneva, Switzerland and the first INCF Congress of Neuroinformatics titled “Databasing and Modeling the Brain”, September 7-9 in Stockholm.

- Molly McElroy, Ph.D.
a freelance science writer based in Washington, DC