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Supplement for Mathematica for Bioinformatics
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1bna.pdb
GFMice.csv
Golub_Files_descriptions.txt
Golub_data_set_ALL_AML_independent.tsv
Golub_data_set_ALL_AML_train.tsv
Golub_table_ALL_AML_samples.doc
Golub_table_ALL_AML_samples.txt
Hu6800_Annotations.tsv
Hu6800_Genes.tsv
MmaBioinfo_Ch10_Networks.nb
MmaBioinfo_Ch11_TimeSeries.nb
MmaBioinfo_Ch12_BioinfoDevelopment.nb
MmaBioinfo_Ch1_Prolog.nb
MmaBioinfo_Ch2_Mathematica.nb
MmaBioinfo_Ch3_Statistics.nb
MmaBioinfo_Ch4_Databases.nb
MmaBioinfo_Ch5_Sequences.nb
MmaBioinfo_Ch6_RNA.nb
MmaBioinfo_Ch7_Protein.nb
MmaBioinfo_Ch8_Metabolites.nb
MmaBioinfo_Ch9_MachineLearning.nb
MmaBioinfo_NotebookIndex.nb
NM_003998.gb
OutputString
README.md
Styles.nb
examplePackage.m
example_sequence.fasta
golubAssociation
golubOmicsObject
golubPhenotypeData
hu6800IDtoAnnotation
outputCSV.csv
sandberg-sampledata.txt
temp
textData.tsv
textfile

README.md

Mathematica for Bioinformatics, by George Mias.

A Wolfram Language Approach to Omics

A Wolfram Language Approach to Omics Springer ISBN 978-3-319-72377-8

Supplementary Files

This repository contains the notebooks(code) and relevant datafiles accompanying the monograph.

Release Notes

  • V.1.0.0 Code updated to monograph release.

Requirements

  • Code was developed and tested under Wolfram Mathematica 11.2.0.0 and also tested in Mathematica 11.3.0.0

Instructions

  • Download either of the Assets to your computer, and use the notebooks in Mathematica as companions to the monograph.
  • All files are best to be kept in the same folder

FAQ

I see a warning regarding compatibility with an older version of Mathematica

  • The code has been checked for compatibility with Mathematica 11.2+, so if you are using a compatible version you can safely ignore the warning.

Some of the results I get from querying the online databases do not match the answers in the notebook

  • The databases queried are updated on a regular basis, and the APIs may also be updated. The code should still work, though you may get more up-to-date responses.

Some of the randomly generated data is different when I run it

  • This is expected (unless RandomSeed is set for reporducibility), as it is highly probably you will get different results from the pseudorandom generator that creates the data in these computations

The UniProt Web API URL used in the notebooks uses https

  • The notebooks have been updated for forward compatibility, since as of release 2018_06 (June 20, 2018) UniProt web pages and services will transition from http to https.

Links

C. OTHER CONTACT INFORMATION

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