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An information environment for neuroscientists

David Wallom

Project background

• JISC Information Environment Programme 2009-2011

• Strand A2: Developing e-Infrastructure to support research disciplines

• Project partners: Oxford, Southampton, Reading

– An e-Research South Consortium project

The Neuroscience partners

• The Oxford group is focused on specific issues such as the study of the molecular basis of synapse formation, plasticity and the regulation of neuronal morphology in the normal and diseased brain. They are examining the mechanisms of an activity-dependent form of neural plasticity known as long-term potentiation (LTP).

• Research at CINN focuses on physiological and psychological mechanisms underpinning complex cognitive behaviours, targeting typical and atypical development and decline in individuals. There is also a strong research group working on issues in signal analysis and computational modelling.

• A focus in Southampton is on the integrative analysis of brain function/dysfunction. Modelling aspects of this across levels of biological organization ranging from molecules, cells, tissue, systems to animal behaviour.

Challenges

• Interdisciplinary teams – different expectations, cultures, requirements

• Agreed standards– Different data formats

Microscopes (Multi-photon or Confocal) Live cell fluorescent imaging Electrophysiology recordings

– Meta data standards• Complexity of tools used in community• Ability to share images, data, analysis• Network connectivity not the best

More Specifically......Help Managing Data

Initial Experimental

Idea

Experimental Design

Data CollectionAnalysis

Publication

Experimental Idea & Design

Microsoft

• Word

• Excel

Shared Documents

Google Docs

Shared Calendar

Experimental Data Collection

Lasersharp 2000

• 2 photon imaging

• Confocal imaging

• Photolysis

Andor IQ

• TIRF

• QD imaging

• Photolysis

Fortran compiler

JAVA

• Modelling

WinWCP/ Strathclyde

• Electrophysiology

Analysis

ClampfitImageJ

OriginMaple

Microsoft Excel

MATLAB

SPSS/InStat

Mathematica

Data Archive Bespoke

Publication/Dissemination

Adobe

• Acrobat

• Photoshop

• Illustrator

Microsoft

• Word

• Excel

Websites

Microsoft PowerPoint

What we would like to see:1. VRE – single point of contact2. A consistent annotation method for data archiving3. Web & shared filesystem based repository for data.

Many file formats to be supported4. A searchable data base for images5. A searchable data base for video images6. A document share tool for ‘live’ manuscript editing7. File space for literature sharing (PDFs)8. Blog area

Release 2.0

• Drupal – Frontend content management. Based on Drupal Commons,

• Alfresco – Backend data management. Modified Alfresco module,

• Apache Solr – Search engine,

• Apache Tika – Metadata extraction toolkit for documents,

• Google services – Docs and Calendar,

• Cloud-based computation using GPU’s,

• NCBO ontology-based tagging,

• LDAP – Single sign-on,

• Digital Pens – Used for recording experiments,

• XML-RPC desktop client – uploading and generating content.

What is Alfresco?

• Open source document management system (also enterprise edition),

• Alternative to Microsoft Sharepoint,

• It provides the following features:

– Unified repository – Manages documents, images, video, audio,

etc…

– Network share services – CIFS/Samba, WebDAV, IMAP and

SharePoint protocol.

– Connectivity – CMIS, JSR 168, REST, Microsoft Office integration.

– Version control – Tracking of major and minor document

versions.

– Folder-based Rules and Actions – Support for document

workflows.

What is Apache Solr?

• Open source search platform based on Apache Lucene,

• Apache Solr search platforms features include:

– Full-text searching,

– Faceted searching,

– Dynamic clustering,

– Database integration,

– Caching and replication,

– Document handling via Apache Tika– e.g. Word, PDF, etc…

– Connectivity – HTTP/XML, JSON API

What is Apache Tika?

• Open source content analysis toolkit,

• Detection and extraction of metadata and structured text from various documents,

– Compressed formats – tar, jar, zip, bzip2, gz, tgz.

– Text Documents – Word, Excel, Powerpoint, RTF, PDF, HTML,

XHTML, OpenDocument, Plain text.

– Images – BMP, GIF, PNG, JPEG, TIFF.

– Audio – MP3, AIFF, AU, MIDI, WAV.

• Extensible parser – Allows for custom parsers to be developed for

other document types.

Architecture

Digital microscope

Electro-physiology

rig

Digital pens

PCWorkflows

Drupal

Continuous integration

AlfrescoGoogle

Services

Site Usage

• Oxford:– Have tested different input methods including digital pens, iPad

and tablet PC.– Uploads of their 6000 image files is working fine, with ~250GB of

data stored.• Reading:

– Want to use NeuroHub as a frontend for their whole centre.– Workflow development has improved scientists working pattern

and supported integration with other complex activities.• Southampton:

– Have ~100GB of data stored and have started to organise their files.

– Interested in digital pen input and want to continue uploading their files in NeuroHub.

Demonstrable Features

• Groups – CINN• Lab Books – Southampton• File system & browsing - Laptop• Shared Calendaring – Platt Lab instance• Searching - Southampton• Livescribe Integration - Laptop• Other content

– Blogs– Documents– Discussions– Wikis

• Taxonomy Manager - CINN• Timeline - Development