Applications & Tools

Network Analysis and Visualization

  1. Arena3Dweb - Interactive 3D visualization of multilayered graphs
  2. NORMA - Network annotation visualization
  3. NAP - Topological network analysis and comparison
  4. VICTOR - Visual analytics for clustering comparison
  5. SARS-CoV-2 protein proximal interactome - novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms
  6. HipMCL - Parallel implementation of MCL clustering
  7. Medusa3 - Visualization of Multi-edge graphs

Text-Mining

  1. DARLING - Disease-bioentity associations with literature mining
  2. OnTheFly2.0 - Document Annotation and Biological Information Extraction
  3. EXTRACT - Interactive Extraction of Metadata from web pages - (developed by Pafilis and Jensen labs)
  4. PREGO - Linking microbes, environments, and processes
  5. UniRed - Protein clustering based on literature
  6. BioTextQuest - Biomedical Literature Clustering

Genomics/Metagenomics

  1. Flame - Functional enrichment for multiple lists
  2. SCALA - A web application for multimodal analysis of single cell next generation sequencing data
  3. NMPfamDB - A database of Novel Metagenome Protein Families
  4. PASTIS - Extreme-scale many-against-many protein similarity search
  5. Meander - Visualization of genome variations
  6. ProteoSign - Proteomics analysis platform
  7. Human Gene Correlation Analysis (HGCA) - Gene clustering based on co-expression patterns
  8. Human gpDB - Signal transduction - CPCRs-proteins-effectors