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This is git repository for the Cytoscape 3 clustering app: clusterMaker


  1. Fix BiClusterView
  2. Add support for BiClustering routines:
  • Cheng & Church
  • BiMine
  • BicFinder
  1. New potential cluster algorithms
  • CIDR (Lin, Troup, Ho, Genome Biology 2017)
  • SPICi (Speed and Performance In Clustering)

7 JUNE - 23 AUGUST 2021 Google Summer of Code by Maija Utriainen

Implementing remote dimensionality reduction techniques using similar approach to last years remote network clusterers (see below).

  • Dimensionality reduction techniques added: Isomap, Local Linear Embedding, MDS, Spectral, tSNE, UMAP
  • Changes to ClusterJobExecutionService and RemoteServer: abstracting and replacing code to another class
  • Subclasses to ClusterJobHandler specific to network clusterers and dimensionality reduction techniques
  • The new algorithms registered in CyActivator

The added and edited code can be found in clusterMaker2/src/main/java/edu/ucsf/rbvi/clusterMaker2/internal/

  • utils/remoteUtils
    • RemoteServer
    • ClusterJobExecutionService
    • NetworkClusterJobHandler
    • DimensionalityReductionJobHandler
  • algorithms/dimensionalityRedcution
    • isomap
    • linearEmbedding
    • mds
    • spectral
    • tSNERemote
    • umap
  • CyActivator

1 JUNE - 29 AUGUST 2020 changes done as a Google Summer of Code Project by Maija Utriainen

Implementing new algorithms with a new approach that runs the algorithm remotely on a server instead of in clusterMaker/Cytoscape utilizing interfaces in package.

  • The algorithms: Leiden, Infomap, Fast Greedy, Leading Eigenvector, Label Propagation, Multilevel
  • The classes used to carry out the remote clustering job are found in remoteUtils. Most of these classes are extended from interfaces and classes and are: ClusterJob, ClusterJobData, ClusterJobDataService, ClusterJobExecutionService, ClusterJobHandler and RemoteServer.
  • The algorithms and ClusterJobExecutionService registered in CyActivator.

My code can be found in several packages in clusterMaker2/src/main/java/edu/ucsf/rbvi/clusterMaker2/internal/

  • utils/remoteUtils
  • algorithms/networkClusterers
    • Leiden
    • Infomap
    • FastGreedy
    • LeadingEigenVector
    • LabelPropagation
    • Multilevel
  • CyActivator