This item is in: Biomedicine > Bioinformatics, computing and life sciences

Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond

Edited by L Harland, Pfizer and M Forster, Syngenta, UK

Woodhead Publishing Series in Biomedicine No. 16

 - discusses a broad range of applications from a variety of sectors
 - provides a unique perspective on work normally performed behind closed doors
 - highlights the criteria used to compare and assess different approaches to solving problems
 - describes implementation of viable practical solutions
 - allows the reader to assess whether the strategies adopted by others could also work in their own organisation

The free/open source approach has grown from a minor activity to become a significant producer of robust, task-orientated software for a wide variety situations and applications. To life science informatics groups, these systems present an appealing proposition - high quality software at a very attractive price. Open source software in life science research considers how industry and applied research groups have embraced these resources, discussing practical implementations that address real-world business problems.

The book is divided into four parts. Part one looks at laboratory data management and chemical informatics, covering software such as Bioclipse, OpenTox, ImageJ and KNIME. In part two, the focus turns to genomics and bioinformatics tools, with chapters examining GenomicsTools and EBI Atlas software, as well as the practicalities of setting up an ‘omics’ platform and managing large volumes of data. Chapters in part three examine information and knowledge management, covering a range of topics including software for web-based collaboration, open source search and visualisation technologies for scientific business applications, and specific software such as DesignTracker and Utopia Documents. Part four looks at semantic technologies such as Semantic MediaWiki, TripleMap and Chem2Bio2RDF, before part five examines clinical analytics, and validation and regulatory compliance of free/open source software. Finally, the book concludes by looking at future perspectives and the economics and free/open source software in industry.

ISBN 1 907568 97 2
ISBN-13: 978 1 907568 97 8
October 2012
582 pages  234 x 156mm  hardback  
£170.00 / US$290.00 / €205.00

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About the editors

Lee Harland is currently leading the information engineering group at Pfizer – a group tasked with developing cutting edge software that helps scientists use internal and external information more effectively. He is also leading member of the pharma-industry pre-competitive group, the Pistoia Alliance, and has 13 years’ experience in bioinformatics, software development and information science within major Pharma.

Mark Forster is currently a senior information domain specialist within the Syngenta R&D Information Systems (RDIS) group, supporting R&D scientists in the fields of small molecule discovery and development, plant breeding and biotechnology. He has 15 years of industrial experience in scientific software development, deployment and support in the US and the UK.

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Contents

Introduction

Building research data handling systems with open source tools
Claus Stie Kallesøe
 - Introduction
 - Legacy
 - Ambition
 - Path chosen
 - The ’ilities
 - Overall vision
 - Lessons learned
 - Implementation
 - Who uses LSP today?
 - Organisation
 - Future aspirations
 - References

Interactive predictive toxicology with Bioclipse and OpenTox
Egon Willighagen, Roman Affentranger, Roland C. Grafström, Barry Hardy, Nina Jeliazkova and Ola Spjuth
 - Introduction
 - Basic Bioclipse–OpenTox interaction examples
 - Use Case 1: Removing toxicity without interfering with pharmacology
 - Use Case 2: Toxicity prediction on compound collections
 - Discussion
 - Availability
 - References

Utilizing open source software to facilitate communication of chemistry at RSC
Aileen Day, Antony Williams, Colin Batchelor, Richard Kidd and Valery Tkachenko
 - Introduction
 - Project Prospect and open ontologies
 - ChemSpider
 - ChemDraw Digester
 - LearnChemistry
 - Conclusion
 - Acknowledgments
 - References

Open source software for mass spectrometry and metabolomics
Mark Earll
 - Introduction
 - A short mass spectrometry primer
 - Metabolomics and metabonomics
 - Data types
 - Metabolomics data processing
 - Metabolomics data processing using the open source workflow engine, KNIME
 - Open source software for multivariate analysis
 - Performing PCA on metabolomics data in R/KNIME
 - Other open source packages
 - Perspective
 - Acknowledgements
 - References

Open source software for image processing and analysis: picture this with ImageJ
Rob Lind
 - Introduction
 - ImageJ
 - ImageJ macros: an overview
 - Graphical user interface
 - Industrial applications of image analysis
 - Summary
 - References

Integrated data analysis with KNIME
Thorsten Meinl, Bernd Jagla and Michael R. Berthold
 - The KNIME platform
 - The KNIME success story
 - Benefi ts of ‘professional open source’
 - Application examples
 - Conclusion and outlook
 - Acknowledgments
 - References

Investigation-Study-Assay, a toolkit for standardizing data capture and sharing
Philippe Rocca-Serra, Eamonn Maguire, Chris Taylor, Dawn Field, Timo Wittenberger, Annapaola Santarsiero and Susanna-Assunta Sansone
 - The growing need for content curation in industry
 - The BioSharing initiative: cooperating standards needed
 - The ISA framework – principles for progress
 - Lessons learned
 - Acknowledgments
 - References

GenomicTools: an open source platform for developing high-throughput analytics in genomics
Aristotelis Tsirigos, Niina Haiminen, Erhan Bilal and Filippo Utro
 - Introduction
 - Data types
 - Tools overview
 - C++ API for developers
 - Case study: a simple ChIP-seq pipeline
 - Performance
 - Conclusion
 - Resources
 - References

Creating an in-house ’omics data portal using EBI Atlas software
Ketan Patel, Misha Kapushesky and David P. Dean
 - Introduction
 - Leveraging ’omics data for drug discovery
 - The EBI Atlas software
 - Deploying Atlas in the enterprise
 - Conclusion and learnings
 - Acknowledgments
 - References

Setting up an ’omics platform in a small biotech
Jolyon Holdstock
 - Introduction
 - General changes over time
 - The hardware solution
 - Maintenance of the system
 - Backups
 - Keeping up-to-date
 - Disaster recovery
 - Personnel skill sets
 - Conclusion
 - Acknowledgements
 - References

Squeezing big data into a small organisation
Michael A. Burrell and Daniel MacLean
 - Introduction
 - Our service and its goals
 - Manage the data: relieving the burden of data-handling
 - Organising the data
 - Standardising to your requirements
 - Analysing the data: helping users work with their own data
 - Helping biologists to stick to the rules
 - Running programs
 - Helping the user to understand the details
 - Summary
 - References

Design Tracker: an easy to use and fl exible hypothesis tracking system to aid project team working
Craig Bruce and Martin Harrison
 - Overview
 - Methods
 - Technical overview
 - Infrastructure
 - Review
 - Acknowledgements
 - References

Free and open source software for web-based collaboration
Ben Gardner and Simon Revell
 - Introduction
 - Application of the FLOSS assessment framework
 - Conclusion
 - Acknowledgements
 - References

Developing scientifi c business applications using open source search and visualisation technologies
Nick Brown and Ed Holbrook
 - A changing attitude
 - The need to make sense of large amounts of data
 - Open source search technologies
 - Creating the foundation layer
 - Visualisation technologies
 - Prefuse visualisation toolkit
 - Business applications
 - Other applications
 - Challenges and future developments
 - Reflections
 - Thanks and acknowledgements
 - References

Utopia Documents: transforming how industrial scientists interact with the scientific literature
Steve Pettifer, Terri Attwood, James Marsh and Dave Thorne
 - Utopia Documents in industry
 - Enabling collaboration
 - Sharing, while playing by the rules
 - History and future of Utopia Documents
 - References

Semantic MediaWiki in applied life science and industry: building an Enterprise Encyclopaedia
Laurent Alquier
 - Introduction
 - Wiki-based Enterprise Encyclopaedia
 - Semantic MediaWiki
 - Conclusion and future directions
 - Acknowledgements
 - References

Building disease and target knowledge with Semantic MediaWiki
Lee Harland, Catherine Marshall, Ben Gardner, Meiping Chang, Rich Head and Philip Verdemato
 - The Targetpedia
 - The Disease Knowledge Workbench (DKWB)
 - Conclusion
 - Acknowledgements
 - References

Chem2Bio2RDF: a semantic resource for systems chemical biology and drug discovery
David Wild
 - The need for integrated, semantic resources in drug discovery
 - The Semantic Web in drug discovery
 - Implementation challenges
 - Chem2Bio2RDF architecture
 - Tools and methodologies that use Chem2Bio2RDF
 - Conclusions
 - References

TripleMap: a web-based semantic knowledge discovery and collaboration application for biomedical research
Ola Bildtsen, Mike Hugo, Frans Lawaetz, Erik Bakke, James Hardwick, Nguyen Nguyen, Ted Naleid and Christopher Bouton
 - The challenge of Big Data
 - Semantic technologies
 - Semantic technologies overview
 - The design and features of TripleMap
 - TripleMap Generated Entity Master (‘GEM’) semantic data core
 - TripleMap semantic search interface
 - TripleMap collaborative, dynamic knowledge maps
 - Comparison and integration with third-party systems
 - Conclusions
 - References

Extreme scale clinical analytics with open source software
Kirk Elder and Brian Ellenberger
 - Introduction
 - Interoperability
 - Mirth
 - Mule ESB
 - Unifi ed Medical Language System (UMLS)
 - Open source databases
 - Analytics
 - Final architectural overview
 - References
 - Bibliography

Validation and regulatory compliance of free/open source software
David Stokes
 - Introduction
 - The need to validate open source applications
 - Who should validate open source software?
 - Validation planning
 - Risk management and open source software
 - Key validation activities
 - Ongoing validation and compliance
 - Conclusions
 - References

The economics of free/open source software in industry
Simon Thornber
 - Introduction
 - Background
 - Open source innovation
 - Open source software in the pharmaceutical industry
 - Open source as a catalyst for pre-competitive collaboration in the pharmaceutical industry
 - The Pistoia Alliance Sequence Services Project
 - Conclusion
 - References