Local Installation

Please note, some basic computer skills are required. If you have difficulties to follow these steps, please find a bioinformatician or IT supporting staff in your department for help.

System Requirements:

  1. OS: Mac OS X, Linux (i.e. Redhat Fedora, Ubuntu)
  2. Memory: >= 4G
  3. Java: 1.7
  4. R: (version >3.4) with the following packages installed:
    "Rserve", "limma", "vsn", "edgeR", "DESeq2", "lattice", "Cairo","igraph", "MCL", "stringr", "RColorBrewer", "data.table", "compiler", "globaltest", "preprocessCore", "sva", "compiler", "RJSONIO", "Rstne", "RSQLite"
  5. Application Server: Glassfish v4+ or Payara v4+.

Local Installation:

  1. Download the NetworkAnalyst Web Application Resource (.war) file here.
  2. Download the NetworkAnalyst knowledgebase (.zip) file here.
  3. Start Rserve from a terminal > R CMD Rserve
    Note: the permission of the web deployment folder must be set properly to give Rserver to Read/Write. It is best to leave the Rserve terminal open. Many R related messages (i.e. progress, exceptions or errors) will be displayed there.
  4. Start the Glassfish/Payara application server.
  5. Deploy the war file via the GUI admin console.
  6. Unzip the knowledgebase and move all five library files into the "/resources/data/" under the deployment folder.
  7. Access your local copy of NetworkAnalyst at: http://localhost:8080/NetworkAnalyst/

External Requests

Gene lists generated from other tools or databases can be sent to NetworkAnalyst using the specified API below:

dataType: "html",
type: "POST",
url: 'http://www.networkanalyst.ca/faces/NAER_LIST',
data: {
    organism: org.code, 
    idtype: id.code, 
    genes: gene.list

organism: the three letters org.code: hsa - H. sapiens (human) mmu - M. musculus (mouse) rno - R. norvegicus (rat) cel - C. elegans (roundworm) dme - D. melanogaster (fruitfly) dre - D. rerio (zebrafish) sce - S. cerevisiae (yeast) bta - B. taurus (cow) gga - G. gallus (chicken) cjo - C. japonica (japanese quail) eco - E. coli bsu - B. subtilis pae - P. aeruginosa mtb - M. tuberculosis tbr - T. brucei (trypanosoma) pfa - P. falciparum (malaria) ath - A. thaliana (Arabidopsis) idtype: entrez is the primary ID in NetworkAnalyst. Generic and organism-specific id.code are given below: Human gene IDs: entrez - Entrez ID refseq - RefSeq ID genbank - Genbank ID symbol - Official Gene Symbol emblgene - Ensembl Gene ID embltranscript - Ensemble Transcript ID emblprotein - Ensembl Protein ID hgu95a - Affymetrix Human Genome U95 (chip hgu95a) hgu95av2 - Affymetrix Human Genome U95 (chip hgu95av2) hgu95b - Affymetrix Human Genome U95 (chip hgu95b) hgu95c - Affymetrix Human Genome U95 (chip hgu95c) hgu95d - Affymetrix Human Genome U95 (chip hgu95d) hgu95e - Affymetrix Human Genome U95 (chip hgu95e) hgu133a - Affymetrix Human Genome U133 (chip hgu133a) hgu133b - Affymetrix Human Genome U133 (chip hgu133b) hgu133plus2 - Affymetrix Human Genome U133plus2 (hgu133plus2) hgu133plus2pm - Affymetrix Human Genome U133plus2_PM (hgu133plus2pm) lumiht12v3 - Illumina HumanHT-12 V3 BeadArray lumiht12v4 - Illumina HumanHT-12 V4 BeadArray lumiref8v2 - Illumina HumanRef-8 V2 BeadArray lumiref8v3 - Illumina HumanRef-8 V3 BeadArray lumiwg6v2 - Illumina HumanWG-6 V2 BeadArray lumiwg6v3 - Illumina HumanWG-6 V3 BeadArray agi4100a - Agilent Human 1 cDNA Microarray (4100A) agi4101a - Agilent Human 2 cDNA Microarray (4101A) agi4110b - Agilent Human 1A cDNA Microarray (4110B) agi4111a - Agilent Human 1B cDNA Microarray (4111A) agi4112a - Agilent Human Genome Whole Microarray (4x44k/4112) agi4845a - Agilent Human AMADID 026652 Microarray (4845A) Mouse gene IDs: entrez - Entrez ID refseq - RefSeq ID genbank - Genbank ID symbol - Official Gene Symbol emblgene - Ensembl Gene ID embltranscript - Ensemble Transcript ID emblprotein - Ensembl Protein ID lumiwg6v1 - Illumina MouseWG-6 v1.0 Bead Array lumiwg6v2 - Illumina MouseWG-6 v2.0 Bead Array lumiref8v1 - Illumina MouseRef-8 v1.0 Bead Array lumiref8v2 - Illumina MouseRef-8 v2.0 Bead Array mgu74a - Affymetrix Murine Genome U74v2 (chip mgu74a) mgu74av2 - Affymetrix Murine Genome U74v2 (chip mgu74av2) mgu74b - Affymetrix Murine Genome U74v2 (chip mgu74b) mgu74bv2 - Affymetrix Murine Genome U74v2 (chip mgu74bv2) mgu74c - Affymetrix Murine Genome U74v2 (chip mgu74c) mgu74cv2 - Affymetrix Murine Genome U74v2 (chip mgu74cv2) moe430a - Affymetrix Mouse Expression Set 430 (chip moe430a) moe430b - Affymetrix Mouse Expression Set 430 (chip moe430b) moe430_2 - Affymetrix GeneChip Mouse Genome 430 2.0 mgi_st1 - Affymetrix Mouse Gene 1.0 ST Array mgu4101a - Agilent Mouse Array (chip mgug4104a) mgu4120a - Agilent Mouse Array (chip mgug4120a) mgu4121a - Agilent Mouse Array (chip mgug4121a) mgu4122a - Agilent Mouse Array (chip mgug4122a) Generic IDs: entrez - Entrez ID emblgene - Ensembl Gene ID embltranscript - Ensembl Transcript ID uniprot - Uniprot Protein ID symbol - Official Gene Symbol In addition to the generic IDs, the specific id.code are supported for the organisms below: Fruitfly: flybase - Flybase ID Yeast: orfid - Open Reading Frame Identifiers Arabidopsis: tair - Tair ID P. aeruginosa: paelocus - Locus Tag E. coli: ecogene - Ecocyc Gene ID genes: same format as NetworkAnalyst gene list input. A small example data is shown below (first column: Entrez ID, second column: fold change): 5743 24.25 3552 21.85 6364 14.64 3553 13.07 10148 10.87 6349 9.19 3620 -8.38 50486 -7.25 2919 -6.96 3557 -6.4 629 -6.07 27074 -6.02
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