Process design for natural scientists
Subtitle: an agile model-driven approach
By: Anna-Lena Lamprecht, Tiziana Margaria (ed.).
Contributors: Margaria-Steffen, Tiziana, 1964- editor
Series: Communications in Computer and Information Science -- 500; Communications in computer and information science -- 500.
Publisher: Springer
Published: 2014
Place of publication: Heidelberg
Language: eng
Number of pages: 253
ISBN-13: 9783662450062; 9783662450055
Subjects: Science; Data processing
Description: This book presents an agile and model-driven approach to manage scientific workflows. The approach is based on the Extreme Model Driven Design (XMDD) paradigm and aims at simplifying and automating the complex data analysis processes carried out by scientists in their day-to-day work. Besides documenting the impact the workflow modeling might have on the work of natural scientists, this book serves three major purposes: 1. It acts as a primer for practitioners who are interested to learn how to think in terms of services and workflows when facing domain-specific scientific processes. 2. It provides interesting material for readers already familiar with this kind of tools, because it introduces systematically both the technologies used in each case study and the basic concepts behind them. 3. As the addressed thematic field becomes increasingly relevant for lectures in both computer science and experimental sciences, it also provides helpful material for teachers that plan similar courses.
Notes: Includes author index.

English.
Table of contents: title: Intro; Preface I; Preface II; Contents; Framework; Scientific Workflows and XMDD; 1 Introduction; 2 Extreme Model-Driven Design of Scientific Workflows; 3 Our Experience So Far; 4 Relationship to Other Scientific Workflow Systems; 5 Outline of the Book; References; Modeling and Execution of Scientific Workflows with the jABC Framework; 1 Introduction; 2 Process and Workflow Modeling in the jABC; 2.1 Common SIBs; 2.2 SIB Taxonomies; 2.3 SLG Execution; 2.4 SLG Validation and Verification; 2.5 SLG Compilation and Deployment; 3 Service Integration: jETI, REST and Web Services; title: 3.1 Integrating Web Services3.2 Electronic Tool Integration; 4 Conclusion; References; The Course's SIB Libraries; 1 Introduction and Overview; 2 The Bioinformatics SIBs Collections; 2.1 ebi-sibs Library (18): SIBs for EBI Web Services; 2.2 pfam-sibs Library (6): SIBs for Pfam Web Services; 2.3 forester-sibs Library (1): SIBs for the Forester API; 3 The Geoinformatics SIBs Collections; 3.1 gmt-sibs Library (7): SIBs for the Generic Mapping Tools (GMT); 3.2 csiss-sibs Library (67): SIBs for the CSISS Web Services; 3.3 geoplugin-sibs Library (4): SIBs for the Geoplugin Web Services; title: 3.4 gisgraphy-sibs Library (6): SIBs for the Gisgraphy Web Services3.5 lbm-sibs Library (9): SIBs for Location-Based Mapping Services; 4 SIBs Collections for Other Functionality; 4.1 ftp-sibs Library (2): SIBs for FTP Operations; 4.2 jeti-helper-sibs Library (9): SIBs for Working with jETI Services; 4.3 openoffice-sibs Library (21): SIBs for Accessing OpenOffice Functionality; 4.4 rest-sibs Library (5): SIBs for General REST Web Service Access; 4.5 twitter-sibs Library (1): SIBs for Accessing Twitter; 4.6 qrcode-sibs Library (3): SIBs for Reading and Writing QR Codes; 5 Conclusion; References; title: Lessons Learned1 Introduction; 2 Domain Modeling; 2.1 Shopping for Service Functionality; 2.2 Service Access; 3 Service Integration; 3.1 Service Interfaces; 3.2 Incomplete or Missing Documentation; 3.3 Changing Interfaces; 4 Workflow Design: The jABC Framework; 5 Workflow Metrics; 5.1 jABCstats: Empirical Analysis of jABC Workflows; 5.2 Results; 6 Conclusion; References; Bioinformatics Applications; Protein Classification Workflow; 1 Introduction: Workflow Scenario; 2 Service Analysis; 3 Workflow Realization; 4 Conclusion; References; Data Mining for Unidentified Protein Sequences; title: 1 Introduction2 Service Analysis; 2.1 Sequence Alignments; 2.2 Optimal Pairwise Alignment; 2.3 Substitution Matrices and Gap Penalties; 2.4 Blast; 2.5 MaFFT; 2.6 InterProScan; 2.7 Phyre; 3 Workflow Realization; 3.1 Blast and Multiple Alignment; 3.2 InterProScan; 3.3 Phyre; 4 Conclusion; References; Workflow for Rapid Metagenome Analysis; 1 Introduction: Workflow Scenario; 2 Service Analysis; 3 Workflow Realization; 3.1 Basic Readin and Setup; 3.2 EST Clustering; 3.3 ORF Prediction and Clustering; 3.4 Pfam Annotation; 4 Conclusion; References; Constructing a Phylogenetic Tree