Open Source Software in Life Science Research

1st Edition

Practical Solutions to Common Challenges in the Pharmaceutical Industry and Beyond

Editors: Lee Harland Mark Forster
Hardcover ISBN: 9781907568978
eBook ISBN: 9781908818249
Imprint: Woodhead Publishing
Published Date: 31st October 2012
Page Count: 582
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Institutional Access

Table of Contents


List of figures and tables


About the editors

About the contributors


Chapter 1: Building research data handling systems with open source tools


1.1 Introduction

1.2 Legacy

1.3 Ambition

1.4 Path chosen

1.5 The ‘ilities

1.6 Overall vision

1.7 Lessons learned

1.8 Implementation

1.9 Who uses LSP today?

1.10 Organisation

1.11 Future aspirations

Chapter 2: Interactive predictive toxicology with Bioclipse and OpenTox


2.1 Introduction

2.2 Basic Bioclipse-OpenTox interaction examples

2.3 Use Case 1: Removing toxicity without interfering with pharmacology

2.4 Use Case 2: Toxicity prediction on compound collections

2.5 Discussion

2.6 Availability

Chapter 3: Utilizing open source software to facilitate communication of chemistry at RSC


3.1 Introduction

3.2 Project Prospect and open ontologies

3.3 ChemSpider

3.4 ChemDraw Digester

3.5 Learn Chemistry Wiki

3.6 Conclusion

3.7 Acknowledgments

Chapter 4: Open source software for mass spectrometry and metabolomics


4.1 Introduction

4.2 A short mass spectrometry primer

4.3 Metabolomics and metabonomics

4.4 Data types

4.5 Metabolomics data processing

4.6 Metabolomics data processing using the open source workflow engine, KNIME

4.7 Open source software for multivariate analysis

4.8 Performing PCA on metabolomics data in R/KNIME

4.9 Other open source packages

4.10 Perspective

4.11 Acknowledgments

Chapter 5: Open source software for image processing and analysis: picture this with ImageJ


5.1 Introduction

5.2 ImageJ

5.3 ImageJ macros:


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 of 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.

Key Features

  • 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


Information and informatics processionals across the field of life sciences; Non-IT professionals with a remit concerning business practices and new technologies


No. of pages:
© Woodhead Publishing 2012
Woodhead Publishing
eBook ISBN:
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About the Editors

Lee Harland Editor

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.

Affiliations and Expertise


Mark Forster Editor

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.

Affiliations and Expertise

Syngenta, UK