Bits, Brains and Behaviors

• The science - NeuronBank

• The history of the project

• What did we learn?

Big Theme – Collaboration

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Common theme• More than just store information• Analysis - increase our understanding of

biological processes• Applying computationally intensive techniques

(e.g., pattern recognition, data mining, machine learning algorithms, and visualization) to achieve this goal.

• Sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction

http://www.cajal.csic.es/V

Understanding the brain requires understanding its circuitry

Problem: We are using publications as a method to catalog neurons

and neural circuits

• Information is distributed and fragmented.• No means to efficiently search this

knowledge.• No means to publish incremental

knowledge without a functional story.

Neuromics

• Genomics is the study of the Genome, where the Genome consists of all of the genes in an organism

• Neuromics is the study of the Neurome, where the Neurome consists of all of the neurons in an organism

The Neurome is harder to represent than the Genome.

• Neurons are identified based on their properties.– Idiosyncratic– Species-specific– Constantly evolving

The Neurome is harder to represent than the Genome.

• No standards for representing our knowledge of neural circuits.

• No means to database this knowledge

Our Approach

• Traditional databases are not a good fit - Changes in representation would cause the database schema to change

• Ontology: A formal representation of a set of concepts within a domain and the relationships between those concepts – A Vocabulary

• We created a core ontology that applies to all nervous systems

• We also support extensible species-specific ontologies.

• NeuronBank is to neurons what GenBank is to genes.– A place to publish knowledge about neurons

and neural connectivity– Tools to represent, search, analyze, and

share knowledge of neurons and neural circuitry.

– Collection of ontologies and tools to access them

NeuronBank.org: A Neuromics Tool

NeuronBank.org: A Neuromics Tool

NeuronBank.org: A Neuromics Tool

DSI

NeuronBank.org: A Neuromics Tool

DSI

NeuronBank.org: A Neuromics Tool

NeuronBank.org: A Neuromics Tool

Lesson 0: (Obvious) Cross-Disciplinary

Challenges• Different disciplines

• Different cultures/languages

• Reward: The satisfaction of working on real problems

• Key: Realistic expectations.

Lesson 1:Defining Requirements

• Requirements describe in detail what a software system is supposed to do

• Easier said than done

• The Myth of Stable Requirements– Specially true in a research project such as

this– Give and take of size/scope through the

funding process

Example: NeuroViz

• Moved from a 3D program to a 2D web browser based applet

• That:

• Became this

NeuronBank v2.0

• NeuronBank 1.0 achieved its objectives.

• First system to:– Support a varying data model for Species specific

representation– While still allowing searches across species

• At the time of commencing work on v1.0 no clear standards existed for storing data as per our requirements

Problems with v1.0

• Since v1.0 a lot of research has gone towards realizing the Semantic Web

• Extension to the WWW where the semantics of the information is defined

• We used a combination of technologies to build v1.0

• This works… But:– Standards have now emerged for the Semantic Web

(OWL) and Biological Ontologies (OBO). We need to conform to these.

– Development Challenges. – Interface problems.

Lesson 2: Design for Change

• Need to design for change• It’s the only thing that’s a given• Projects should have the ability to evolve,

discard and replace individual components with minimal impact on other pieces– Going from a stand alone 3-D Viz Tool to a

browser based tool meant several changes for the branch

– Moving to a Semantic Web version

Lesson 3: Community Building is hard

• A lot of excitement every time we pitch this to a group of researchers working on some species.

• But who will enter the data? 80/20 rule• The system is only as good as what’s in it.• Some sort of an incentive is needed to get

new species started– Using NeuronBank wiki in classes– Then moving this data into NeuronBank

• Some visible advantage to using the system

Cerebral Ganglia

Lesson 4: Managing Humans

• Who owns this?– Code– Project/Sub-project

• Academic Attrition• Publication potential to keep students

interested– Ideally enough research for this to be the

honors/thesis/dissertation topic for a student

Lesson 5: Institutional support

• Was this a good investment?

• $36,000 - 2004 Seed Grant:

• $25,976 - 2005 2nd Seed Grant:

• $61,976 - Total initial investment by GSU

• $258,102 - Funded Grants (R21 grant)– (4x initial investment)

• $1,873,102 – NSF and NIH– (30x initial investment)

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Past MembersAkshaye Dhawan(now at Ursinus College)Bob Calin-Jageman,(now at Dominican University)Jason PamplinHao TianHong YangHsui Wang Janaka BalasooriyaXiuyun ShenWenjun MaPiyaphol PhoungpholNaveen Hiremath Monika PatelSuzy Gentner

Neuroscience Institute Paul Katz

Computer ScienceSushil Prasad, Ph.D.Ying Zhu, Ph.D.Raj Sunderraman, Ph.D.

Students:•Chad Frederick•Weiling Li•Rasanjalee Dissanayaka Mudiyanselage•Shuman Gao

Thank You for your time and attention

Questions?