Difference between revisions of "Software"

From Bioinformatics Lab
Jump to: navigation, search
(Network-based servers for Disease Research)
(Bacteria)
(34 intermediate revisions by 5 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
=='''Co-functional networks and hypothesis generation servers'''==
+
=='''Gene Regulation Research Tools'''==
 +
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse
  
==''Human and Animals''==
+
 
 +
 
 +
 
 +
 
 +
=='''Network Medicine Tools '''==
 +
[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data
 +
 
 +
 
 +
[[File:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data
 +
 
 +
 
 +
 
 +
[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
 +
 
 +
 
 +
 
 +
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms
 +
 
 +
 
 +
 
 +
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)
 +
 
 +
 
 +
 
 +
 
 +
 
 +
=='''Co-functional Gene Networks'''==
 +
 
 +
==''Human and Laboratory Animals''==
 
{|border="0"  width="500"
 
{|border="0"  width="500"
 
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
 
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
Line 20: Line 49:
 
{|border="0"  width="400"
 
{|border="0"  width="400"
 
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
 
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
 +
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
 
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
 
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
 +
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
 
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
 
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
 
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
 
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
 
 
|-
 
|-
 
|align="center"|''Arabidopsis thaliana''
 
|align="center"|''Arabidopsis thaliana''
 +
|align="center"|''Zea mays''
 
|align="center"|''Oryza sativa''
 
|align="center"|''Oryza sativa''
 +
|align="center"|''Triticum aestivum''
 
|align="center"|''Glycine max''
 
|align="center"|''Glycine max''
 
|align="center"|''Solanum lycopersicum''
 
|align="center"|''Solanum lycopersicum''
|align="center"|''Triticum aestivum''
 
 
|}
 
|}
  
Line 44: Line 75:
 
{|border="0"  width="200"
 
{|border="0"  width="200"
 
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
 
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
 +
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]
 +
|align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]]
 
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
 
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
 
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
 
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
 
|-
 
|-
|align="center"|''Pseudomonas aeruginosa''
+
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
|align="center"|''Escherichia coli''
+
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
|align="center"|''Xanthomonas oryzae pv. oryzae''
+
|align="center"|''Klebsiella pneumoniae (human pathogen)''
 +
|align="center"|''Escherichia coli (popular lab/factory bacterial species)''
 +
|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''
 
|}
 
|}
  
 
+
==''Build your own co-functional networks''==
 
+
 
+
=='''Build your co-functional networks for all other species'''==
+
 
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
 
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
'''JiffyNet:Instant gene network building server for newly sequenced species'''
+
'''JiffyNet''': Instant gene network building server for newly sequenced species
  
  
  
  
=='''Network-based servers for Disease Research'''==
 
[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)'''
 
  
 
[[File:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB: a web server for network-based boosting of human genome-wide association data'''
 
 
 
[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN: cancer gene discovery via network analysis of somatic mutation data'''
 
 
 
 
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN: Network-assisted prediction of disease pathways in model organisms'''
 
 
=='''Other Network Biology tools'''==
 
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining): A reference database of human TF-target interactions'''
 
  
  
 +
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
 +
[[WMI|<big>'''Project Page'''</big>]]
  
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE (Reflective diffusion and local extension): Network-assisted Gene Set Analysis (human only)'''
 
  
 
+
=='''Domain2Pathway by Pathway Specificity (PS) '''==
 
+
[[PS|<big>'''Project Page'''</big>]]
 
+
 
+
 
+
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
+
[[WMI|<big>'''Project Page'''</big>]]
+

Revision as of 17:11, 21 December 2017

Gene Regulation Research Tools

TRRUST logo.jpg TRRUST: A reference database of TF-target interactions in human and mouse



Network Medicine Tools

Cover title muffinn.png MUFFINN: Cancer gene discovery via network analysis of somatic mutation data


GWAB logo.png GWAB: A web server for network-based boosting of human genome-wide association data


Coexpedia.png COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)


Logo morphin.png MORPHIN: Network-assisted prediction of disease pathways in model organisms


Cover title riddle.jpg RIDDLE: Network-assisted Gene Set Analysis (human only)



Co-functional Gene Networks

Human and Laboratory Animals

Tools HumanNetLogo.jpg MouseNetLogo.png Danionet logo.png Flynet.png WormNetv3.jpg
Homo sapiens Mus musculus Danio rerio Drosophila melanogaster Caenorhabditis elegans

Plants

Aranet v2.jpg Maizenet logo 4th.png RiceNetv2 logo.png WheatNet logo.png Soynetlogo.png Tomatonet logo.png
Arabidopsis thaliana Zea mays Oryza sativa Triticum aestivum Glycine max Solanum lycopersicum

Fungi

Tools YesatNetLogo.jpg CryptoNet.png
Saccharomyces cerevisiae Cryptococcus neoformans

Bacteria

Pseudomonas logo.jpg Staphnet logo.JPG KlebNet logo.png EcoliNet.png XooNet logo.png
Pseudomonas aeruginosa (human pathogen) Methicillin-resistant Staphylococcus aureus (human pathogen) Klebsiella pneumoniae (human pathogen) Escherichia coli (popular lab/factory bacterial species) Xanthomonas oryzae pv. oryzae (rice pathogen)

Build your own co-functional networks

Jiffynetlogo4 small.jpg JiffyNet: Instant gene network building server for newly sequenced species




Domain-based PPI networks by Weighted Mutual Information (WMI)

Project Page


Domain2Pathway by Pathway Specificity (PS)

Project Page

Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox