Mathematica for Bioinformatics: A Wolfram Language Approach to Omics
Saved in:
| Main Author: | |
|---|---|
| Format: | Electronic eBook |
| Language: | English |
| Published: |
Cham
Springer International Publishing
2018
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| Subjects: | |
| Online Access: | BTU01 HTW01 UBR01 UBW01 Volltext Inhaltsverzeichnis |
| Physical Description: | 1 Online-Ressource (XVI, 384 p. 175 illus., 156 illus. in color) |
| ISBN: | 9783319723778 |
| DOI: | 10.1007/978-3-319-72377-8 |
Staff View
MARC
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| 245 | 1 | 0 | |a Mathematica for Bioinformatics |b A Wolfram Language Approach to Omics |c by George Mias |
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| 650 | 4 | |a Life sciences | |
| 650 | 4 | |a Microarrays | |
| 650 | 4 | |a Bioinformatics | |
| 650 | 4 | |a Systems biology | |
| 650 | 4 | |a Biostatistics | |
| 650 | 4 | |a Metabolism | |
| 650 | 4 | |a Computational biology | |
| 650 | 4 | |a Life Sciences | |
| 650 | 4 | |a Computer Appl. in Life Sciences | |
| 650 | 4 | |a Metabolomics | |
| 650 | 4 | |a Microarrays | |
| 650 | 4 | |a Systems Biology | |
| 650 | 4 | |a Computational Biology/Bioinformatics | |
| 650 | 4 | |a Biostatistics | |
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Record in the Search Index
| _version_ | 1804178433878523904 |
|---|---|
| adam_text | Contents
1 Prolog: Bioinformatics with the Wolfram Language 1
1 1 Bioinformatics in Modem Genetics 1
1 2 Scope of This Monograph 2
1 3 Prerequisites 3
1 4 Presentation of Input and Output and Graphics 3
1 5 Accompanying Notebooks 5
References 6
2 A Wolfram Language Primer for Bioinformaticians 7
2 1 Getting Started 7
211 Hello World 7
212 Hello to Wolfram]Alpha 10
213 Getting Started Resources 10
2 2 Syntax 12
2 3 Variables 13
2 4 Basic Mathematical Operations 14
2 5 Type Casting 16
2 6 Algebra 17
2 7 Lists 18
271 Collections of Expressions 18
272 List Element Extraction 21
273 Ordered Lists with Table 22
274 Element Manipulation 22
275 List Manipulation 23
276 Matrices 24
2 8 Functions 26
281 SetDelayed 27
282 Transformation Rules 28
283 Defining Functions 30
284 Options 31
IX
X
Contents
2 9 Programming Essentials 32
291 Comments 32
292 Boolean Operations and Flow 32
293 Modules, Blocks and With 36
294 Patterns 38
295 Pure Functions and Slots 40
296 Function Manipulation 42
2 10 Strings 44
2 10 1 Character Codes 46
2 10 2 Sequences as Strings 47
2 11 Importing and Exporting Data 48
2 11 1 Importing Files 48
2 11 2 Streams 51
2 12 Associations and Datasets 54
2 13 Exceptions 56
2 14 Graphical Capabilities 57
2 15 Additional Capabilitities Through Packages 61
2 15 1 Importing Packages 61
2 15 2 MathlOmica 62
References 65
3 Statistics 67
31A Primer for Statistics with the Wolfram Language 67
3 2 Descriptive Statistics 67
33A Short Probabilistic Sequence of Events 69
3 4 Examples of Discrete Distributions 72
341 Bernoulli Distribution 72
342 Binomial Distribution 75
343 Geometric Distribution 78
344 Poisson Distribution 80
345 Hypergeometric Distribution 80
3 5 Examples of Continuous Distributions 85
351 Uniform Distribution 85
352 Exponential Distribution 87
353 Normal Distribution 88
354 Chi-Squared Distribution 94
355 Student-t Distribution 95
3 6 Other Distributions 96
3 7 Data Sets 97
371 ExampleData 97
372 ResourceData 104
373 Entity Types 106
374 Data Example: The Golub ALL AML Data Set 108
Contents
xi
375 Example: Sandberg et al Data by Pavlidis Ill
376 Example: Marcobal et al 113
377 Example Data: MathlOmica 114
3 8 Hypothesis Testing 115
381 Location Tests 116
382A High-Level Approach 120
3 9 Additional Statistics 120
391 Expectations and Correlations 120
392 Moments of a Distribution 125
393 Distribution Fit 127
References 131
4 Databases: E-Utilities and UCSC Genome Browser 133
4 1 Connecting to Databases 133
4 2 NCBI Entrez Programming Utilities 134
421 EInfo 134
422 ESearch 137
423 EPost 147
424 ESummary 149
425 EFetch 152
426 ELink (Entrez Links) 154
427 EGQuery 160
428 ESpell 161
429 ECitMatch 162
4 2 10 API Keys and Usage Guidelines 162
4 3 UCSC Genome Browser 163
431 Sequence Retrieval 163
432 Sequence Retrieval Details 163
References 170
5 Genomic Sequence Data and BLAST 171
5 1 Sequences of Genomic Information 171
5 2 Parsing Files 174
521 FASTA Sequences 174
522 GenBank Records 176
5 3 Sequence Alignment 179
5 4 BLAST(n) 182
541 BLAST API Parameter List 182
542 Running Web Based BLAST Example 1 183
543 BLAST Example 2 188
References 192
Contents
xii
6 Transcriptomics Examples 193
6 1 Transcriptomic Analysis 193
6 2 Golub ALL AML Training Set 193
621 Golub Original Set Normalization 195
622 Golub ALL AML Combined Dataset 198
623 Golub Annotations 203
624 Leukemia Differential Expression Analysis 205
6 3 Analysis of Variance for Multiple Tests 213
References 225
7 Proteomic Data 227
7 1 Amino Acids 227
7 2 Protein Information 237
7 3 UniProt 237
731 Individual Entry Retrieval 237
732 Query Entry Retrieval 239
733 Executing Queries 240
734 Random Entry Generation 242
735 Identifier Mapping 242
7 4 NCBI Entrez Utils 243
741 Sequence Retrieval 243
742 From Sequence to Protein 244
743 Search by Molecular Weight 246
7 5 Proteins Sequence Alignment 246
751 SequenceAlignment 247
752 BLASTp 248
References 250
8 Metabolomics Example 251
8 1 Metabolomics Data 251
8 2 Germ Free and Inoculated Mice Data 251
821 Processing Imported Data 252
8 3 Principal Component Analysis 257
8 4 Differential Analysis GF Versus 5 Days After Inoculation 262
8 5 Identifying Compounds Using ChemSpider 268
8 6 Identifying Compounds and Pathway Analysis: KEGG 274
References 280
9 Machine Learning 283
91A Taste of Clustering 283
9 2 Dimensional Reduction 285
9 3 Classification 286
9 4 The Iris Data Classified Across Methods 289
References 296
Contents
xiii
10 Graphs and Networks 297
10 1 Introduction to Graphs 297
10 1 1 Vertices and Edges 297
10 2 Basic Graph Construction 300
10 2 1 Entering a Graph 300
10 2 2 Defining Weighted Graphs 305
10 3 Basic Graph Properties 306
10 3 1 Degree 307
10 3 2 Adjacency Matrix 308
10 3 3 Weighted Adjacency Matrix 310
10 4 Some More Definitions 311
10 4 1 Walks and Paths 311
10 4 2 Graph Geometry 312
10 4 3 Centrality 313
10 4 4 Clustering Coefficient 314
10 5 Graph Examples 315
10 5 1 Empty Graphs 315
10 5 2 Complete Graphs 316
10 5 3 Regular Graphs 318
10 5 4 Cycle Graphs 319
10 5 5 Trees 321
10 5 6 Bipartite Graphs 321
10 6 Isomorphisms 322
10 7 Random Graphs 324
10 7 1 Barabasi Albert Distribution 325
10 7 2 Watts Strogatz 326
References 328
11 Time Series Analysis 329
11 1 Time Series 329
11 1 1 The TimeSeries Function 329
11 1 2 Multiple Time Series Example 333
11 2 Vignette: FinancialData 338
11 3 Time Series Model Fitting 339
11 3 1 USA BMI Data Modeling 341
11 4 Unevenly Sampled Time Series Classification Examples 349
11 4 1 Lomb Scargle Classification in MathlOmica 349
11 4 2 Classification Simulation Example 350
11 4 3 Classification RNA Sequencing Data Example 353
11 4 4 Heatmaps and Dendrograms 364
References 372
XIV
Contents
12 Epilog: Bioinformatics Development with Mathematica 375
12 1 Bioinformatics Development With the Wolfram
Language 375
12 2 Loading Packages 375
12 3 The examplePackage 376
12 3 1 Contexts 377
12 4 Odds and Ends 379
12 4 1 More Information on Packages 379
12 4 2 Dynamic Interfaces and Manipulate 379
12 5 The Wolfram Language Community 380
References 380
|
| any_adam_object | 1 |
| author | Mias, George |
| author_facet | Mias, George |
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| dewey-ones | 570 - Biology |
| dewey-raw | 570.285 |
| dewey-search | 570.285 |
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| dewey-tens | 570 - Biology |
| discipline | Biologie |
| doi_str_mv | 10.1007/978-3-319-72377-8 |
| format | Electronic eBook |
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| id | DE-604.BV044888695 |
| illustrated | Not Illustrated |
| indexdate | 2024-07-10T08:03:54Z |
| institution | BVB |
| isbn | 9783319723778 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-030282751 |
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| physical | 1 Online-Ressource (XVI, 384 p. 175 illus., 156 illus. in color) |
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| publishDate | 2018 |
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| publisher | Springer International Publishing |
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| spelling | Mias, George Verfasser aut Mathematica for Bioinformatics A Wolfram Language Approach to Omics by George Mias Cham Springer International Publishing 2018 1 Online-Ressource (XVI, 384 p. 175 illus., 156 illus. in color) txt rdacontent c rdamedia cr rdacarrier Life sciences Microarrays Bioinformatics Systems biology Biostatistics Metabolism Computational biology Life Sciences Computer Appl. in Life Sciences Metabolomics Systems Biology Computational Biology/Bioinformatics Erscheint auch als Druck-Ausgabe 978-3-319-72376-1 https://doi.org/10.1007/978-3-319-72377-8 Verlag URL des Erstveröffentlichers Volltext HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030282751&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Mias, George Mathematica for Bioinformatics A Wolfram Language Approach to Omics Life sciences Microarrays Bioinformatics Systems biology Biostatistics Metabolism Computational biology Life Sciences Computer Appl. in Life Sciences Metabolomics Systems Biology Computational Biology/Bioinformatics |
| title | Mathematica for Bioinformatics A Wolfram Language Approach to Omics |
| title_auth | Mathematica for Bioinformatics A Wolfram Language Approach to Omics |
| title_exact_search | Mathematica for Bioinformatics A Wolfram Language Approach to Omics |
| title_full | Mathematica for Bioinformatics A Wolfram Language Approach to Omics by George Mias |
| title_fullStr | Mathematica for Bioinformatics A Wolfram Language Approach to Omics by George Mias |
| title_full_unstemmed | Mathematica for Bioinformatics A Wolfram Language Approach to Omics by George Mias |
| title_short | Mathematica for Bioinformatics |
| title_sort | mathematica for bioinformatics a wolfram language approach to omics |
| title_sub | A Wolfram Language Approach to Omics |
| topic | Life sciences Microarrays Bioinformatics Systems biology Biostatistics Metabolism Computational biology Life Sciences Computer Appl. in Life Sciences Metabolomics Systems Biology Computational Biology/Bioinformatics |
| topic_facet | Life sciences Microarrays Bioinformatics Systems biology Biostatistics Metabolism Computational biology Life Sciences Computer Appl. in Life Sciences Metabolomics Systems Biology Computational Biology/Bioinformatics |
| url | https://doi.org/10.1007/978-3-319-72377-8 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030282751&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT miasgeorge mathematicaforbioinformaticsawolframlanguageapproachtoomics |