项目作者: bioasp

项目描述 :
:arrow_upper_right: Influence graph analysis, consistency check, diagnosis, repair and prediction
高级语言: Rust
项目地址: git://github.com/bioasp/iggy.git
创建时间: 2014-07-30T18:36:51Z
项目社区:https://github.com/bioasp/iggy

开源协议:GNU General Public License v3.0

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iggy + optgraph Build Status

iggy and optgraph are tools for consistency based analysis of influence graphs and observed systems behavior (signed changes between two measured states). For many (biological) systems are knowledge bases available that describe the interaction of its components in terms of causal networks, boolean networks and influence graphs where edges indicate either positive or negative effect of one node upon another.

iggy implements methods to check the consistency of large-scale data sets and provides explanations for inconsistencies. In practice, this is used to identify unreliable data or to indicate missing reactions. Further, iggy addresses the problem of repairing networks and corresponding yet often discrepant measurements in order to re-establish their mutual consistency and predict unobserved variations even under inconsistency.

optgraph confronts interaction graph models with observed systems behavior from multiple experiments. opt_graph computes networks fitting the observation data by removing (or adding) a minimal number of edges in the given network.

Downloads

Compile yourself

Clone the git repository:

  1. git clone https://github.com/bioasp/iggy.git
  2. cargo build --release

The executables can be found under ./target/release/

Iggy

Typical usage is:

  1. iggy -n network.cif -o observation.obs -l 10 -p

For more options you can ask for help as follows:

  1. > iggy -h
  2. iggy 2.2.1-dev
  3. Sven Thiele <sthiele78@gmail.com>
  4. Iggy confronts interaction graph models with observations of (signed) changes between two measured
  5. states (including uncertain observations). Iggy discovers inconsistencies in networks or data,
  6. applies minimal repairs, and predicts the behavior for the unmeasured species. It distinguishes
  7. strong predictions (e.g. increase in a node) and weak predictions (e.g., the value of a node
  8. increases or remains unchanged)
  9. USAGE:
  10. iggy [OPTIONS] --network <FILE>
  11. OPTIONS:
  12. -a, --auto-inputs Declare nodes with indegree 0 as inputs
  13. --depmat Combine multiple states, a change must be explained by an
  14. elementary path from an input
  15. --elempath Every change must be explained by an elementary path from an
  16. input
  17. --founded-constraints-off Disable foundedness constraints
  18. --fwd-propagation-off Disable forward propagation constraints
  19. -h, --help Print help information
  20. --json Print JSON output
  21. -l, --show-labelings <N> Show N labelings, default is OFF, 0=all
  22. --mics Compute minimal inconsistent cores
  23. -n, --network <FILE> Influence graph in CIF format
  24. -o, --observations <FILE> Observations in bioquali format
  25. -p, --show-predictions Show predictions
  26. --scenfit Compute scenfit of the data, default is mcos
  27. -V, --version Print version information

Optgraph

Typical usage is:

  1. optgraph -n network.cif -o observations_dir/ --show-repairs 10

For more options you can ask for help as follows:

  1. > optgraph -h
  2. optgraph 2.2.1-dev
  3. Sven Thiele <sthiele78@gmail.com>
  4. Optgraph confronts interaction graph models with observations of (signed) changes between two
  5. measured states. Opt-graph computes networks fitting the observation data by removing (or adding) a
  6. minimal number of edges in the given network
  7. USAGE:
  8. optgraph [OPTIONS] --network <FILE> --observations <DIR>
  9. OPTIONS:
  10. -a, --auto-inputs Declare nodes with indegree 0 as inputs
  11. --depmat Combine multiple states, a change must be explained by an
  12. elementary path from an input
  13. --elempath Every change must be explained by an elementary path from an
  14. input
  15. --founded-constraints-off Disable foundedness constraints
  16. --fwd-propagation-off Disable forward propagation constraints
  17. -h, --help Print help information
  18. --json Print JSON output
  19. -m, --repair-mode <REPAIR_MODE> REPAIR_MODE: remove = remove edges (default), optgraph = add
  20. + remove edges, flip = flip direction of edges
  21. -n, --network <FILE> Influence graph in CIF format
  22. -o, --observations <DIR> Directory of observations in bioquali format
  23. -r, --show-repairs <N> Show N repairs, default is OFF, 0=all
  24. -V, --version Print version information