1000 genomes project, 252, 508, 521

Active Directory, 242, 268

Adobe Acrobat, 354

Adverse Events Reporting System database (AERS), 52, 61

agile development, 271

agrochemicals, 2, 5

alerting, 45, 346, 404, 443, 450, 492

Altmetric, 363, 365

AlzSWAN, 410, 420

Amazon, 327, 468–9, 472, 480

AMES test, 44

clinical Analytics, 7, 453–5, 457, 459, 461, 463, 465, 467, 469, 471, 473–5, 477–9

clinical data, 365, 386, 453, 465, 475

AnnoJ 273–5, 283

Apache, 17, 33, 156, 253–4, 260, 272, 278–9, 283, 285, 289–91, 295–7, 303, 322, 327–8, 330, 349–50, 419, 452, 468, 471, 477, 479–80, 505, 515

Apache Tika, 328, 330, 349

ArrayExpress, 60, 187, 224, 229, 233

ASK query, 401, 406, 413–14

AstraZeneca, 39, 285–7, 290–1, 325–8, 332–3, 335–6, 338, 341–2, 344, 347, 349

Asynchronous JavaScript and XML (AJAX), 19, 253, 289

backup, 121, 129, 241–2, 245, 247, 249–50, 260, 295, 500

Bacula 245–6, 260

Basic Local Alignment Search Tool (BLAST) 250–1, 254, 270, 283

BeanShell, 138

Beowulf, 242

BGZip, 252, 260

big data, 6, 22, 217, 263, 265, 267, 271, 273, 275, 277, 279, 281, 283, 435–7, 439, 441–2, 451, 453, 468–9, 476

bigData database, 445

Bingo 69–70, 86, 281

Bioclipse, 5, 35–61, 490, 504

Biolnvestigation Index, 180, 183

BioJava, 169, 255, 258, 261, 425, 430, 490, 504

BioLDA, 431

BioLinux, 180, 187

Biological Process Maps 341–2

biomarker, 188, 223, 237, 240, 392, 408, 412

BioPerl, 255, 260, 490, 504

BioPortal, 180, 187, 226, 238, 426

BioSharing, 173, 175–6, 186–7

BLAST-Like Alignment Tool (BLAT), 243, 254

blog, 272, 293, 299–300, 304–9, 322–3, 352, 354, 363, 371, 377, 380, 505, 521

microblogging, 299, 304–9

Broad Institute, 252, 283

business intelligence, 7, 475

business model, 4, 6–7, 125, 157, 391, 505, 513

cancer, 44, 190, 200, 219, 227, 233, 235, 253, 326–7, 344, 406, 474, 506

Cassandra 471–2, 480

Chem2Bio2RDF, 6, 59, 421–7, 429–33

ChemBioGrid, 422, 425

ChEMBL 43–4, 422, 426

ChemDoodle, 71, 82–3, 86

ChemDraw Digester 72–4, 76–7

Chemical entities of biological interest (ChEBI), 66, 183, 188

chemical structure, 9, 21, 31–2, 35–6, 45–6, 66, 69–70, 73, 76, 86, 91, 432

cheminformatics/chemogenomics, 34, 60–1, 63–4, 70, 83, 151, 158, 297, 422, 424–6, 429–30, 432–3, 452

Chemistry Development Kit 39–40, 43, 61, 66–7, 85–6, 160, 425

chemometrics, 60, 90, 115–16, 125, 128

ChemSpider 63–5, 67–75, 77–85, 107, 357, 365, 422

ChlP-Seq, 168, 189–90, 193, 196–7, 207–8, 210–11, 213, 215, 219, 229

Clojure, 138

cloud computing, 15, 125, 246, 505, 512

commercial vendors, 64, 124–5, 157, 170, 245, 258–9, 481, 487, 514

competitor intelligence, 401, 407

Compound Design Database, 287

compute cluster, 108, 112, 115–16, 120, 156–7, 169, 242–3, 276–8, 285, 289, 295–6, 298, 328, 385, 431–2, 441, 444, 469, 471–2, 474, 476

copyleft, 2, 33

copyright, 2, 361–3

corporate database 9–11, 16, 158–9, 231

CouchDB, 461, 470, 479–80

crystallography, 64, 85

curation, 68, 79–80, 84, 173–4, 179–81, 183, 185–7, 221, 225–6, 232–5, 379, 412, 441

cytogenetics, 239

Cytoscape, 121, 128, 430

CytoSure, 255, 260

D2R Server, 427

data integrity, 491, 496

data mining, 10, 113, 129, 158, 237, 353, 409, 422, 424, 433, 474

data warehouse, 10, 32, 386, 397, 454

Debian, 17, 33, 266, 276, 283

decision tree, 152, 168

Design Tracker, 6, 285–7, 289, 291–7

diagnostic, 116, 239–40, 479

disambiguation, 183, 315, 329–32, 378–80

disaster contingency (disaster planning, point of failure)

disease resistance, 266

disk array 241–3, 246, 249

Django, 285, 291–2, 296, 298

Documentum, 320, 443

DokuWiki, 245, 260

drug repositioning, 325, 339, 341

drug target, 235, 391–2, 394, 397, 407, 419

Dryad, 363, 365

Eclipse platform, 112, 128, 151, 155, 253, 260

electronic lab notebook, 511

Ensembl, 216, 220, 250, 252, 260, 281, 283, 392, 396, 419

Enterprise Research Data Management, 11

enterprise search, 367, 369, 378–9, 384, 388, 450, 452

European Bioinformatics Institute (EBI), 183, 221–9, 231–5, 237, 250

European Federation of Pharmaceutical Industries and Associations (EFPIA), 181, 188

European Molecular Biology Open Software Suite (EMBOSS), 251, 260, 490, 504

Experimental Factor Ontology, 226, 233, 238

Extensible Stylesheet Language Transformations (XSLT), 67, 71, 461

Extjs, 19, 22–3, 33

faceted search, 327, 336, 348

failover, 285, 291, 294–5, 347

FAST search, 450

FASTA, 171, 270–1, 275, 282, 445, 499

FASTQ 168–9, 216, 251, 260, 270–1, 283

Fiji, 134, 138

Firefox, 23, 72, 275, 505–6

Flare, 334, 348

Flex, 334, 341, 369

freedom to operate, 29

Galaxy, 187, 190, 219, 276–9, 281–3

GBrowse, 169, 171, 273, 281

Gene Expression Atlas, 5, 221–2, 224, 231–2, 238

gene set enrichment analysis (GSEA), 327, 384, 387, 425, 436

GeneData, 183, 188

GenePix, 254, 260

General Public License (GPL) 1–2, 19, 33, 63, 90, 128, 133, 151, 190, 275, 305, 377, 382, 466, 470, 482

GeneSpring, 224, 254–5

Genome Analysis ToolKit, 252, 260

geospatial search, 328

GGA Software, 34, 69–70, 82–4, 86, 160, 171, 278, 394, 466

GGobi, 125, 129

Git, 19, 21, 32–3, 185, 188

GlaxoSmithKline (GSK), 28, 44, 90, 124, 257, 261, 301, 349

Google File System, 468, 480

Google Patents, 70, 86

Groovy, 40, 253

Hadoop, 453, 468, 476–7, 480

HBase, 2, 10, 471, 507

Health Level Seven International (HL7), 453, 455–9, 463–4, 474, 479

high availability, 285, 291, 296

high content imaging, 266

histopathology, 186

HTML5 71–2, 85, 389, 504

Human Genome Project, 506

HUPO Proteomics Standards Initiative, 95, 183

ICD10 (International Classification of Diseases), 453, 479

Illumina, 229, 265, 270, 282

image analysis, 127, 131–2, 139, 146–9, 267, 273

ImageJ, 5, 131–45, 147–9

Imglib, 158, 164, 171

InChI, 38, 45, 66–9, 72, 81–2, 85, 87, 207, 211, 427

Indigo, 153, 158, 160, 171

InfoVis, 334

Innovative Medicines Initiative (IMI), 30, 181, 186

Integrated Genome Viewer, 273

Investigation Study Assay (ISA), 173, 176–81, 183, 185–7

Java Universal Network Graph, 334

Javascript Object Notation (JSON), 227, 271, 274–5, 283, 328, 372–3, 383, 398, 472

JBrowse, 273, 275, 283

JChemPaint, 70, 86

Johnson and Johnson, 369, 374, 385

JSpecView, 63, 71, 82–3, 86

Ketcher, 21, 32, 34, 70, 82, 86

KnowIt 374–6, 380, 382–9

Knowledge Management, 6, 59, 79, 188, 320, 342, 356, 362, 367–8, 370, 379, 381, 389, 391, 409–10, 418, 435, 442, 446, 448–50

Konstanz Information Miner (KNIME), 5, 58, 61, 89, 112–15, 117, 126–8, 131, 139–40, 149, 151–3, 155–9, 161–4, 166–71, 339, 490, 504

Laboratory Information Management Laboratory Information Management Systems (LIMS), 121, 271

LAMP Stack, 17, 33, 126, 285, 303

Latent Dirichlet Allocation, 431

Learn Chemistry 78–80, 83, 87

licencing, 12, 19, 31, 124–5, 132–3, 245, 251, 254–5, 258, 289, 326, 483, 495, 509, 513–15, 521

Life Science Platform (LSP), 9, 30–2, 520

Lightweight Directory Access Protocol (LDAP), 151, 307, 334, 372, 394

Linked Data, 6, 16, 29–30, 34, 46, 48, 58–9, 61, 69, 82, 84, 169, 180, 187, 274, 367, 369–70, 382–5, 388–9, 418, 421–7, 429–33, 435, 437, 439–46, 448–52, 457, 479, 519

RDF, 6, 16, 29–30, 46, 48, 59, 69, 82, 169, 187, 274, 383–5, 389, 421–7, 429–33, 435, 439–44, 452, 457, 519

triple store, 30, 382–5, 423, 425, 427, 430, 440–1, 445

semantic web, 6, 34, 58–9, 61, 84, 180, 367, 385, 388–9, 418, 421–4, 432, 439, 452, 479

SPARQL, 43, 382–6, 389, 423, 425, 427, 430, 440, 443, 452

Linux, 1, 17, 19, 33, 95, 121, 133, 151, 155–6, 180, 187, 232, 241–4, 247, 253, 257, 268, 285, 289–90, 295–8, 303, 484, 505, 510, 515

Lucene/SOLR, 6, 322, 325, 327–33, 336, 339, 341, 344, 346–50, 397, 419, 437, 452

Lundbeck 9–14, 16, 18, 21, 23–5, 27–33

machine learning, 34, 61, 125, 152

macro 131–3, 136–45, 147–9, 314

Malware, 518

MapReduce 468–9, 472–3, 476–80

Markush structure, 76

Mass spectroscopy, 5, 89–95, 97, 99, 101, 103, 107, 109, 113, 115, 117, 119, 121, 123, 125–9, 179, 183, 265, 482

MATLAB, 116, 138

Maven, 124

MediaWiki, 6, 30, 59, 78–83, 86–7, 285, 290–1, 297, 299, 313–18, 322–3, 367, 369–71, 373–9, 381–9, 391, 393–5, 397–8, 401, 407, 409, 411, 413, 415, 417–20

Medical Subject Headings (MeSH), 3, 132, 331, 339, 349, 397, 404, 420, 435, 476, 512, 519

medicinal chemistry, 24, 61, 68, 286–7, 292–4, 401

metabolomics, 5, 89–91, 93–5, 97, 99, 101, 103–4, 106–9, 112–15, 117, 119, 121, 123–9, 177, 180, 183, 188, 221, 326, 420

metadata, 5, 21, 30, 81, 174–5, 177–81, 186, 224, 233–5, 270–1, 273–4, 276, 330, 333, 348, 354, 363, 385–6, 388, 398, 442, 446, 448, 466, 475

microdata/RDFa, 6, 30, 169, 383, 389, 423, 427, 431–2, 440

Microsoft Excel, 144, 147, 209, 328, 344

Microsoft Windows, 23, 95, 107, 121, 133–4, 151, 155, 199–201, 204–5, 207, 211–12, 241–4, 253, 259, 267–8, 277, 289, 303–5, 307, 312

mind-mapping, 409

Minimum Information Standards 174–5, 183, 185, 187–8, 225

Minimal Information About a Microarray Experiment (MIAME), 183, 188, 225, 237

Mirth 458–63, 478–9

Model-View-Controller 22–3, 34, 271

Mongrel, 272

Moores law, 132, 264, 282

Mozilla Rhino, 138

MSPcrunch, 250, 260

MySQL, 32, 34, 157, 243, 249, 251, 254, 258, 260, 285, 290–1, 294–6, 303, 372, 407, 461, 466–7, 478–80

mzData, 95, 98–9, 101

mzMine, 89, 101–4, 106–8, 112–13, 126–7

mzML, 95, 101, 126

MzXML, 95, 101, 126

National Center for Biotechnology Information (NCBI), 71, 85–6, 252, 258–60, 264, 365, 419–20

National Library Of Medicine (NLM), 71, 464

NetBeans, 253, 260

NetCDF, 95, 101, 226, 228, 232, 238

NetVault 245–6, 260

network attached storage, 246

NeuronJ 133–4, 141, 149

Nginx, 279, 283, 285, 295–6, 298

NIH image 132–3

NMR spectroscopy, 1, 179

NoSQL, 453, 461, 466–9, 471–2, 475, 477–8, 480

Omero 272–3, 282–3

Ondex, 121, 129, 319

ontology 38–9, 43–4, 59, 63–5, 67, 85, 173, 180, 183, 185, 187–8, 196, 201, 213, 220, 225–6, 233, 235, 238, 252, 271, 283, 339, 342, 373, 379, 396, 398, 401, 404, 419–20, 423–7, 430, 456

Ontology of Biomedical Investigations, 183

Open Parser for Systematic IUPAC Nomenclature (OPSIN) 66–7

Open Source Chemistry Analysis Routines (OSCAR) 63–7, 85

Open Source Software Advisory Service, 515

Open Web Application Security Project, 512, 518, 521

OpenBabel, 63, 70, 73–4, 76–7, 86

OpenEye, 84, 291, 296, 298

OpenIdentify, 336

OpenPHACTS 30–1, 34, 84, 87, 357, 365, 423, 432

OpenTox, 5, 35–47, 49–51, 53–61

Oracle 11–13, 16, 21–2, 31–2, 231–2, 251, 258, 260, 296, 397, 466

Oxford Gene Technology, 239

Pareto scaling, 117

patents 69–70, 86, 240, 326, 338, 341, 354, 435, 443–4, 449, 510

pathway, 36, 60, 186, 214, 220, 226–7, 235, 255, 342, 392–6, 401, 404, 406, 408, 413, 415, 417, 421, 423–4, 426, 429, 432, 441

patient, 193, 223, 325–6, 339, 342, 408, 412, 426, 455–8, 468, 471–2, 475, 477, 482–4, 491

PDF 127–9, 149, 162–3, 220, 280, 323, 328, 330, 351, 353–7, 359–63, 365, 417, 419

peak detection, 89, 102–4, 127

Pentaho 475–8, 480

Peregrine, 332, 349

Perl, 12, 17–18, 43, 113, 156, 158, 204, 206, 217, 233, 253, 255, 257, 260, 270, 289, 330, 401, 410, 417, 458, 463, 490, 503–4

pharmacokinetics, 223

Pharmamatrix, 395

php, 78, 80–1, 86–7, 96, 126–7, 129, 171, 253–4, 258, 260, 285, 290–1, 297, 303, 382, 389, 420, 521

Phusion Passenger, 272, 283

Picard, 252, 260

Pipeline Pilot, 334, 339, 349

Pistoia Alliance, 34, 176, 187, 505, 511–14, 517, 520–1

Portland Press, 363

PostGresSQL, 466

pre-competitive, 3, 7, 84, 187, 234–5, 408, 482, 505, 510–11, 520–1

PredTox, 173, 181–3, 186, 188

Prefuse, 334, 342, 344, 346, 348–9

Project Prospect 64–5, 84–5

proteomics, 90, 95, 121, 126, 128, 183, 187–8, 221, 326

provenance, 174, 362, 383, 385, 418

PubChem, 68, 74, 85, 422, 426–7, 429

publisher, 8, 63–5, 67–8, 353–5, 362–4

PubMed 70–1, 86, 331, 346, 365, 372–3, 395, 431, 433, 435

Python, 113, 138, 158, 257, 278, 285, 289, 291–2, 295–7, 317, 330, 349

Quantitative Structure-Activity Relationship (QSAR), 36, 39–40, 45, 58, 60–1, 297, 429

Quick Response Codes 140–1, 148–9

R - scripting and statistics language

R based, 129, 228, 255, 257, 278

R BioConductor, 95, 97, 98, 127, 128, 187, 190, 193, 215, 216, 217, 219, 255, 261, 490, 504

R code, 115, 120

R development, 44, 65, 67, 84, 127, 156, 170, 192, 237, 253, 255, 282, 425, 487

R environment, 11, 39, 40, 209

R foundation, 127, 490, 504

R GUI, 129

R language, 89, 95, 115, 138, 142, 255, 257, 291, 296, 317, 477

R Java, 232, 477

R journal, 129, 355

R Knime, 113, 114, 117

R method, 94, 115, 116, 141

R node, 89, 114, 115, 118, 119, 120, 122, 152, 153, 154, 159, 161, 163, 168, 169, 170, 242, 468, 469

R package, 95, 97, 102, 112, 117, 128, 129, 149, 180, 190, 215, 282

R project, 7, 27, 33, 65, 224, 253, 258, 260, 287, 292, 293, 297, 298, 342, 344, 393, 396, 410, 509

R programming, 255, 334, 477

R regression, 128

R script, 89, 117, 228

R serve, 80, 242, 243, 247, 268, 272, 278, 290, 333, 374, 425, 427, 476, 477

R snipett, 113, 115, 118, 119, 120

R Studio, 95, 98, 253, 260

R statistics / statistical, 39, 89, 95, 107, 127, 138, 158, 190, 205, 229, 258, 341, 504

R suite, 296, 298, 477

R sweave, 125

Rattle, 125, 129

RDKit, 32, 34, 158, 162–3, 171, 490, 504

REACH regulations, 35

Really Simple Syndication (RSS), 280, 309, 315, 346, 373, 381, 404, 435, 443, 448–9

Red Hat, 4, 7, 17, 33, 157, 232, 290, 296–8, 484, 510

regulatory issues, 7, 125, 481–8, 491, 493, 495, 497, 499–500, 504

software validation, 125, 483, 497, 504

regulatory agencies, 484

GAMP, 481, 483–7, 491, 495, 499–500, 504

regulated environment, 7, 125

Eudralex, 483, 488, 493, 499, 504

Representational State Transfer (REST), 18, 60, 66, 71, 226, 334, 472–3, 478

Riak 471–3

Ruby-on-Rails 17–18, 23, 33–4, 138, 271–2, 283

SADI framework, 59, 61

Sainsbury Laboratory, 265, 283

SAM format, 169, 189, 195–6, 204, 220

Samba, 241, 259, 283

SAMtools, 220, 252, 260, 283

SAVANT, 273, 283

scalability 15–16, 265–6, 281, 291, 303, 305, 309, 313–14, 328–9, 382, 432, 441, 444, 454, 466–8, 471, 473, 499, 512

schema, 117, 183, 278, 281, 283, 292, 329, 339, 396, 422, 427, 440, 465–8, 471, 473

SciBorg, 64, 66, 85

Scuttle 309–12, 321, 323

Security, 15, 25, 37, 124–5, 237, 250, 304, 348, 363, 380–1, 425, 455, 476, 496, 500, 505, 510, 512–13, 515–20

Semantic Forms, 371, 376, 379, 413, 420

Semantic Link Association Prediction, 343, 431

Semantic MediaWiki, 6, 30, 59, 81, 314, 367, 369–71, 373–9, 381–9, 391, 393–5, 397, 401, 407, 409, 411, 413, 415, 417–20

semantic search, 389, 423, 435, 442, 444, 446, 450–1

Sequence Services, 34, 511–16

SharePoint, 305, 320, 323, 380–1, 389, 420, 443–4

Simile, 334, 430

Simple Object Access Protocol (SOAP), 56, 71, 381, 446, 476

Single Nucleotide Polymorphism 98–9, 190, 200, 251, 253, 266, 279, 281, 389

SMILES, 43, 45–8, 52–3, 160–1, 290–1, 427

Snoopy, 81, 87

social bookmarking 299–300, 307, 309–12, 317, 323, 371, 380

social networking, 6, 299–300, 309, 311, 388, 407, 418, 431, 482

software as a service, 485, 487

Sourceforge, 60, 85–7, 220, 252, 260, 283, 323, 420, 430, 433, 479, 504, 521

SQL server 66–70, 72, 251, 260

SQLite, 69, 277–8, 283

Stallman, 1, 133

statistical clustering, 108, 112, 116, 120, 328, 385, 432, 444, 469, 472, 474

Status.Net 304–9, 321, 323

storage, 7, 10, 21, 30, 90, 121, 180, 222, 241, 246–7, 266–8, 270, 277, 282, 295, 361, 381–2, 423–5, 436, 440, 445, 453, 465–8, 471–3, 496, 499, 507–8

support vector machine, 116, 152

sustainability, 156, 176, 185, 364

Symyx, 11, 17, 21, 31–2

systems chemical biology, 421, 424, 433

Tabix, 252, 260

tagging, 183, 311, 323, 325, 329, 332–3, 346, 401, 404, 406, 413, 417

Targetpedia, 391, 394–8, 404, 406–7, 410, 412, 418–19, 450

Taverna, 58, 61, 282–3, 339, 490, 504

Text Mining, 59, 64, 67, 175, 353, 355, 357, 359, 363, 365, 395

Third Dimension Explorer 385–6

Tomcat, 232, 253, 260, 328

toxicology, 5, 10, 35–7, 39–41, 43–5, 47, 49, 51–61, 126, 181, 187–8, 222–3, 379, 421, 424, 426, 429, 431

TripleMap, 6, 59, 423, 435, 437, 439, 441–6, 448–51

Tungsten Enterprise, 295

Twitter, 300, 304–5, 323, 325, 448, 452, 474, 480

Unified Medical Language System (UMLS) 463–5, 468, 473, 477–8, 480

URL shortener, 305, 380

US 21CFR Part, 11, 479, 482, 490

Utopia documents, 6, 351, 353–5, 357, 359, 361, 363–5

Variant Effect Predictor, 252

VCFTools, 252, 260

virtual machine, 133, 304, 322

virtual server, 296, 298

Web service, 21, 43, 60, 76, 80, 254, 273–5, 283, 291, 309, 339, 353, 381, 408, 422, 425, 469

Web2.0, 289, 299–300, 303, 310, 319, 322

Weka, 158, 258, 476–7, 480

Wellcome Trust, 3

widget, 21, 183, 430

Wikipedia, 1, 32–3, 41, 78, 80, 87, 126, 149, 248, 260, 282–3, 294, 300, 313, 315, 318, 323, 355, 367–9, 388, 392–6, 401, 419, 433, 480, 506, 521

WordPress, 505

World Wide Web Consortium, 180, 187, 439, 441, 451

XCMS 97–8, 100–1, 127, 129

XML Database, 467

XPath/XQuery, 467

xrite, 148

Yammer, 304, 323