Fourth NeuroML Development Workshop

Convergence in Computational Neuroscience 2012

Joint BrainScaleS CodeJam/NeuroML workshop, Edinburgh, 12-16th March

The NeuroML Development Workshops and the BrainScaleS (previously FACETS) CodeJams have been two important initiatives in recent years for developers of tools in computational and systems neuroscience to present their latest work, exchange ideas and work at achieving interoperability between software applications for investigating brain function. This year these groups held a joint workshop (Convergence in Computational Neuroscience) on March 12th-16th in the Informatics Forum in Edinburgh, UK.

The meeting was held at the Informatics Forum in Edinburgh, UK, from 12th to 16th March 2012.

Meeting report

Note, details of the meeting activities from Wednesday 14th to Friday 16th are available on the NeuralEnsemble.org webpage.


Monday 12th March: NeuroML Development Workshop Day 1

Morning session: Current state of NeuroML 2 development & relationship to other initiatives  Chair: Andrew Davison

09:00Welcome & goals of meeting

Angus welcomed attendees, thanking in particular out local organisers at University of Edinburgh, Mike Hull and Mika Pelko!
 
Angus Silver
09:05Update on latest developments in NeuroML 2/LEMS (PPT)

Padraig presented an introduction to NeuroML, starting with an overview of the modular nature of NeuroML v1.x, advantages of the use of XML, examples of neuronal models in NeuroML, current tools which support the language, (including the recently added NeuroMorpho.org and Channelpedia).

The requirements for v2.0 were presented. Explicit definitions of model component behaviour allows description of the dynamics of model components in a simulator independent, machine readable way. The relationship between LEMS and NeuroML2 was discussed. A short overview of NeuroML 2.0 was given including dimensions/units. Example of adaptive exponential integrate and cell network was presented. An overview of libNeuroML was given. Export to NEURON, neuroConstruct, interaction with SBML was shown.
 
Padraig Gleeson
09:30Introduction to NineML & libNineML (PDF)

Mike gave an introduction to the NineML object model and libNineML. The INCF Task Force in Multiscale Modelling created the language, consisting of an Abstraction Layer and User Layer. Mike's presentation focused on the abstraction layer which contains many terms for the object model. Core object in the Abstraction layer were presented: ComponentClass, Interface with Parameters, Ports (AnalogPorts, EventPorts and Reduce Ports), Dynamics with StateVariables and a Regime Transition Graph (with Transitions, StateAssignments, Aliases).

libNineML (in Python) loads and saves models from/to XML to/from Python that helps with code generation, turns models into NEST, NEURON and PyNN.
 
Mike Hull
10:00The COMBINE Initiative (PDF)

Nicolas presented the Combine Initiative: Standards for describing the whole life-cycle of modelling. Different communities favour different types of models that are more suited for their domain. Current standardisation efforts depend on the initial people, individual funding structure, IP issues. Specifications, API's, test-suites, etc. really need industry-grade support which is not compatible with standard academic usages and possibilities.

The vision of COMBINE is to pave the space of model descriptions with coordination of standard development (without interference with the development). There are criteria for inclusion in the core COMBINE standards: new standards must be different from those already included, described in technical specification documents, free, open, developed and used by more than one team, democratically elected members, mature software support including API, and must be actively developed.

COMBINE organises joint meetings replacing standards specific ones (e.g. SBML Hackathon). Next COMBINE meeting is in Toronto in August. HARMONY for hacking will be in Maastricht in May.
 
Nicolas le Novere
 
10:30Coffee
 
11:00The International Neuroinformatics Coordinating Facility

Sean presented the motivation for, current structure and the aims of the INCF. The goal of neuroscience is to understand the brain. We're at a crisis point in understanding disorders. Big Pharma is pulling out of neuroscience due to the high cost and risk of understanding these disorders. Past centuries have focused on obtaining observations. More recently, models were used to understand these observations. Today we have eScience as a new way of handling large-scale data, modelling, simulations, linking data, etc. One of the INCF's goals is to transform neuroscience into an eScience from level of molecules to clinic.

Integration of databases is a goal, which requires standardized data formats. There are 16 member countries in INCF. He gave an introduction to the 4 programs from the past few years: Digital Brain AtlasingMulti-Scale ModelingOntologies of Neural Structures  and Standards for Datasharing.

He discussed future plans for the INCF "Cyberinfrastructure", including a discussion of the planned INCF cloud "Dropbox" for data which could include metadata tags enabling global search.
 
Sean Hill
11:30Collaborative Modelling Repository update

Padraig presented the initial work towards an open source, collaborative repository for NeuroML models, the Open Source Brain project. A preliminary version of this is avaliable here. It will be based on a version control repository (initially Mercurial) storing the model files. It will have automatic generation of online documentation of the models from ChannelML, MorphML, etc. Connectivity matrices for network connections, etc. can be generated for models which are stored in neuroConstruct format. NeuroLex IDs can be used to identify cells and channels to other resources. Feedback on the initial implementation was welcomed.
 
Padraig Gleeson
12:00Open discussion on model specification initiatives

Differences were pointed out between INCF and COMBINE approaches to standards development. IEEE provides an infrastructure for review, etc. Nicolas discussed the burdens of obtaining "official" standards board recognition. Many of the COMBINE procedures imitate W3C procedures. A good standard is one that works. COMBINE criteria don't say anything about the standard document itself.
 
 
13:00Lunch (provided)

Afternoon session: Specification of detailed biophysical components in NeuroML 2/LEMS  Chair: Sharon Crook

14:00Representing channels, synapses & conductance based models (PDF)

Robert gave a presentation on ways to represent synapses and conductances. He defined the Nernst equation with XML based on Hille's description. It is still not clear how some things should be done, in particular how to handle dimensions and units. Currently, dimensions are defined and then assertions about relationships among dimensions can be made. Units are not defined until NeuroML is written (with numerical values, e.g. -70mV). There was some discussion of how dimensions should be defined. Physicists solved this problem by developing SI units. Both space and no space between values and units are allowed in LEMS. There was some discussion of how events can be handled in LEMS.
 
Robert Cannon
14:20Experiences with using NeuroML 2

Avrama gave a brief report of her hands on experience with using NeuroML 2. She has a medium spiny projection neuron model which she's translating to GENESIS. She didn't want to use a GUI unless absolutely necessary and has been manually editing the XML. Many of the (non calcium dependent) channels have already been converted to NeuroML 2. She can only run single compartment versions of her model since LEMS doesn't yet support multi compartmental models. She has produced some some multi segment morphologies in NML2, even though these can't be used in LEMS based simulations yet. She requires a way to specify distance from the soma. Another difficulty is not being able to define a template (dendritic) subbranch and add it multiple times to the cell. She will add spines later. Calcium dependent channels are a work in progress in NeuroML v2.0, but some useful simulations have already been done with her developing model.
 
Avrama Blackwell
14:40Implementing cerebellar models in PyNEURON, neuroConstruct & NeuroML

Sergio is developing cerebellar models (Golgi cells and granular cells) in a network of granule layer. Solinas S, Nieus T and D`Angelo E (2010) A realistic large-scale model of the cerebellum granular layer predicts circuit spatio-temporal filtering properties. Frontiers in Cellular Neuroscience (link) gives an overview of the network. There were improvements made to the model in 2011 and it was translated to Python Neuron for parallel simulation on cluster. Added gap junctions, more realistic inputs. Python eased improvements to the model.

Points to address: It was very difficult to construct exclusion rules for the complex structure of the network. This was difficult in both NEURON and Python. There must be a procedure for constructing the network since one must look for inhibition first then decide on a connection. Also, for data visualisation, for voltage in space and time for the entire network, it would be useful to have a standard way to do this (also for field potentials). Expressing network structure can be a problem for a declarative format.
 
Sergio Solinas
15:00Large scale cortical models for studying LFPs (PPT)

Richard presented his work on developing large scale cortical models for studying Local Field Potentials. What network properties cause pathological dynamics? Much data comes from electrodes in vitro. Gaute Einevol's work looks at how dendritic structure affects the field potentials in a network (Linden et al Neuron 2010). Richard focused on Bush and Sejnowski J Neurosci Methods 1993 method to reduce model and see what the LFP looks like (and compared to Linden data). Then since it looked pretty good he created a network of these reduced models for simulation and analysis. Then looked at results from Utah array in Matlab. Next he'll add Gaussian connectivity and some patches and long range connections.
 
Richard Tomsett
 
15:15Coffee
 
15:30Breakout sessions:
    Channel and synapse specifications
    Proposed structure for abstract neuron model hierarchy
 
17:30Reconvened and presentated discussions

 
18:00Close
 

Tuesday 13th March: NeuroML Development Workshop Day 2

Morning session: Representing morphologies/support for detailed neuronal simulators/relationship to connectomics initiatives  Chair: Michael Hines

09:00The Neural Tissue Simulator: How to specify and scale an arbitrary number of compartment variables over an arbitrary number of compartments (PDF)

James presented his work on the Neural Tissue Simulator, much of which was contained in the recent publication: Kozloski J and Wagner J (2011) An ultrascalable solution to large-scale neural tissue simulation. Frontiers in Neuroinformatics. 5:15. (link).

The key goals of this work are: to develop a simulator capable of testing mappings to various machine architectures, both parallel and multithreaded; to develop support for high level, abstract model definitions and simulation specifications; and to create an extensible simulator, able to map arbitrary, domain level models directly to a variety of data arrangements and computational implementations.

James discussed the process of defining the model (using the Model Definition & Graph Specification Languages), how the model elements are partitioned on the computing resources, and how these elements communicate during simulation to solve the model equations. He discussed the specific case of simulating cortical columns when synapses were determined through contact detection algorithms. He also presented some results for how the simulator scales for larger networks. The Neural Tissue Simulator is not currently publicly available, but James is keen to make it available, and to build a community of users. NeuroML support is also planned.
 
James Kozloski
09:30The Blue Brain Project

Eilif presented an overview of the Blue Brain Project's efforts to reverse engineer a P14 Rat non-barrel somatosensory cortical column. Based on a database of anatomical reconstructions, electrophysiology, etc. they will fill the cortical column with cells based on known location, probability distributions. Morphologies for those classes of cells are taken from library of cells called a collage with some rules about how they fit in based on constraints from reconstructions. Some of these cells have been "repaired" due to axon cuts in reconstructions.

Functional circuits are also based on biological data. Electrical behaviors are based on classifications based on firing patterns observed in experiments. This is combinatorial since each morphological class has a number of possible firing patterns. They use genetic algorithm to adjust parameters which are set up based on what is known (gene expression, etc). Channelome project uses cell culture and automated patch clamp by robot and then automated model fitting for data that are then posted to Channelpedia. Channels there are available in ChannelML. Synaptic parameterization and validation for functional synapses are also based on database of recorded synaptic properties.

In silico model is compared to in vitro using same protocols as experiments. There was a standards and interoperability discussion: they are mostly using custom formats other than what they use with NEURON. Eilif welcomed greater support for more widely used standards.
 
Eilif Muller
10:00Tools for the dense reconstruction of neuronal circuits

Moritz gave an overview of his recent work with Winfried Denk and Frank Briggman, which is continuing in his own lab. They have used Serial Block-Face Electron Microscopy (SBEM), to investigate the connectivity in blocks of neuronal tissue, which has been the subject of a number of recent publications, e.g. K.L. Briggman, Helmstaedter, M. and W. Denk, Wiring specificity in the direction-selectivity circuit of the mammalian retina. Nature 471, 183-188, 2011. (link).

He also discussed the application KNOSSOS which was developed to facilitate the reconstruction of neuronal morphologies from such data. While this tool uses a proprietary format for storing morphologies, it is open source and Mortiz was keen to integrate the application with other tools using NeuroML.
 
Moritz Helmstaedter
 
10:30Coffee
 
11:00The OpenWorm project: Using NeuroML in a highly detailed model of C. elegans (PPT)

Stephen presented the OpenWorm project. This ambitious project aims to build an in silico model of C. elegans. This well studied system with ~1000 cells and 302 identified neurons is an ideal system with which to attempt a full simulation of a living organism down to cellular scale. Many different approaches are being take in the project at the moment, including investigatin Smoothed Particle Hydrodynamics (SHP) to allow simulation of the interaction of the worm with its environment, and creating a new parallel (GPU based) simulator in Java which will support physical and electrical simulations. Full reconstructions of all of the cells are available in 3D and those of the neurons have been converted to NeuroML, which will form the basis of a simulation of the worm's nervous system.

One of the concrete outcomes of code sprinting work on the fringes of the NeuroML/CodeJam meeting was the updated OpenWorm Browser, where the full cellular structure of the worm can be browsed in 3D.
 
Stephen Larson
11:30Open discussion on tool support for large scale neuronal simulations


 
 
13:00Lunch (provided)

Afternoon session: Best practices when implementing support for NeuroML in simulators  Chair: Avrama Blackwell

14:00Introduction to SED-ML (PDF)

Dagmar gave an overview of the motivation behind the development of SED-ML, the Simulation Experiment Description language , the current status of the specification, and some of the uses it has been put to so far. It compliments a model description in SBML or NeuroML and allow specification of the simulation algorithm used to run the model, any changes made to the parameters specified in the model description, the simulation duration, what variables were saved during the simulation, and how that data was processed.

In SED-ML you can define a uniform time course with an initial time and start and end time. This needs to be expanded to other possible time courses. Multiple tasks (simulations) can be defined. For example, run the original database model and the changed model. Output can be set up as 2D or 3D plots or a datatable. SED-ML has an elected board of editors. Contribution to SED-ML is encouraged. Sourceforge can be used for feature requests and this will move forward as people contribute.
 
Dagmar Waltemath
14:20Introduction to CNO: an ontology for annotating computational neuroscience models (PDF)

Yann presented an introduction to CNO: an ontology for annotating computational neuroscience models. All classes must have a unique identifier, a label (name) and a human-readable definition. Relationships among classes are specified with relations. Examples are subsumption relations, associative relations, etc. We then can associate this semantic information with parts of XML files.

The INCF Task Force in Multiscale Modelling originally wanted to add semantic info to NineML models, but this should be extensible to NeuroML and PyNN models as well. CNO needs to be compatible and interoperable with other ontologies in the OBO community and abide with their recommendations. Protege provides an interface for viewing editing CNO. Currently 210 classes, 8 relationships and 4 datatype properties. Greater integration with NeuroLex and the Systems Biology Ontology is planned.
 
Yann le Franc
14:40NeuroLex & NIF update (PPT)

Stephen gave us an update on NeuroLex and the Neuroscience Information Framework (NIF). We need for an online parts list for the brain. NeuroLex is built on Wiki technology with extra functionality to create structured knowledge where anyone can create or edit. It currently as about 18,000 concepts. NIF funds curators from NIH money and also looks for volunteers. In the future they want to dominate Google searches with NeuroLex terms. Looking to Yelp for how they display info including images and related queries and such. Some place for community comments. Another goal is to expose high quality linked data with example of an open linked data graph.
 
Stephen Larson
15:00libSBML and SBML L3 (PDF)

Sarah gave a brief overview of libSBML and SBML Level 3. libSBML, which provides an API for creating, editing and saving SBML in many languages (e.g. C++, Python, Java, Ruby, Perl) has been instrumental in the growth of the number of applications supporting SBML.

SBML Level 3 has a modular architecture, featuring a core specification (roughly in line with previous SBML releases) and a number of specialist packages, which applications can choose to support or not. Examples of these packages incluse layout for storing the spatial topology of a model's network diagram, comp for defining how a model is composed from other models and spatial for describing models that involve a spatial component. libSBML already has a generic framework to support extensions for generic packages.
 
Sarah Keating
15:15Coffee
 
15:30Breakout sessions:
    How best to map generic model descriptions to a given simulator
    Support for morphologies
17:30Reconvened and presented discussions


 
18:00Close of meeting

Wednesday 14th March - Friday 16th March

Full details of the meetings from Wed-Fri are available on the NeuralEnsemble.org webpage for the meeting.



The NeuroML part of this workshop was made possible with funding from:

    NIH

    Wellcome Trust

    UK INCF Node

    INCF


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