| Description |
1 online resource |
| Series |
Woodhead Publishing series in biomedicine ; 16 |
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Woodhead Publishing series in biomedicine ; no. 16.
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| Contents |
Cover; Open source software in life science research: Practical solutions in the pharmaceutical industry and beyond; Copyright; Dedication; Contents; List of figures and tables; Foreword; About the editors; About the contributors; Introduction; 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; 1.12 References; 2 Interactive predictive toxicology with Bioclipse and OpenTox |
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2.1 Introduction2.2 Basic Bioclipse-Open Tox 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; 2.7 References; 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; 3.8 References; 4 Open source software for mass spectrometry and metabolomics; 4.1 Introduction |
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4.2 A short mass spectrometry primer4.3 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 Acknowledgements; 4.12 References; 5 Open source software for image processing and analysis: picture this with ImageJ; 5.1 Introduction; 5.2 ImageJ; 5.3 ImageJ macros: an overview; 5.4 Graphical user interface |
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5.5 Industrial applications of image analysis5.6 Summary; 5.7 References; 6 Integrated data analysis with KNIME; 6.1 The KNIME platform; 6.2 The KNIME success story; 6.3 Benefits of 'professional open source'; 6.4 Application examples; 6.5 Conclusion and outlook; 6.6 Acknowledgments; 6.7 References; 7 Investigation-Study-Assay, a toolkit for standardizing data capture and sharing; 7.1 The growing need for content curation in industry; 7.2 The BioSharing initiative: cooperating standards needed; 7.3 The ISA framework -- principles for progress; 7.4 Lessons learned; 7.5 Acknowledgments |
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7.6 References8 GenomicTools: an open source platform for developing high-throughput analytics in genomics; 8.1 Introduction; 8.2 Data types; 8.3 Tools overview; 8.4 C++ API for developers; 8.5 Case study: a simple ChIP-seq pipeline; 8.6 Performance; 8.7 Conclusion; 8.8 Resources; 8.9 References; 9 Creating an in-house 'omics data portal using EBI Atlas software; 9.1 Introduction; 9.2 Leveraging 'omics data for drug discovery; 9.3 The EBI Atlas software; 9.4 Deploying Atlas in the enterprise; 9.5 Conclusion and learnings; 9.6 Acknowledgments; 9.7 References |
| Summary |
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 d |
| Bibliography |
Includes bibliographical references and index |
| Notes |
Online resource; title from digital title page (viewed on Jan. 28, 2013) |
| Subject |
Drugs -- Research -- Data processing
|
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Life sciences -- Research -- Data processing
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Open source software.
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Medical Informatics
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Medical Records Systems, Computerized
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MEDICAL -- Pharmacology.
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Drugs -- Research -- Data processing
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Open source software
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| Form |
Electronic book
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| Author |
Harland, Lee.
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|
Forster, Mark
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| LC no. |
2012944355 |
| ISBN |
9781908818249 |
|
1908818247 |
|
