iggy

Tools for consistency based analysis of influence graphs and observed systems behavior

Sign Consistency on Influence Graphs - Diagnosis, Repair, Prediction

iggy + opt_graph

iggy and opt_graph 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.

opt_graph 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:

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

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

Iggy

Typical usage is:

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

For more options you can ask for help as follows:

> iggy -h
iggy 2.1.0
Sven Thiele <sthiele78@gmail.com>
Iggy confronts interaction graph models with observations of (signed) changes between two measured states
(including uncertain observations). Iggy discovers inconsistencies in networks or data, applies minimal
repairs, and predicts the behavior for the unmeasured species. It distinguishes strong predictions (e.g.
increase in a node) and weak predictions (e.g., the value of a node increases or remains unchanged).

USAGE:
    iggy [FLAGS] [OPTIONS] --network <network-file>

FLAGS:
    -a, --auto-inputs               Declare nodes with indegree 0 as inputs
        --depmat                    Combine multiple states, a change must be explained by an
                                    elementary path from an input
        --elempath                  Every change must be explained by an elementary path from an input
        --founded-constraints-off   Disable foundedness constraints
        --fwd-propagation-off       Disable forward propagation constraints
    -h, --help                      Prints help information
        --mics                      Compute minimal inconsistent cores
        --scenfit                   Compute scenfit of the data, default is mcos
    -p, --show-predictions          Show predictions
    -V, --version                   Prints version information

OPTIONS:
    -l, --show-labelings <max-labelings>     Show max-labelings labelings, default is OFF, 0=all
    -n, --network <network-file>             Influence graph in CIF format
    -o, --observations <observations-file>   Observations in bioquali format

Opt_graph

Typical usage is:

> opt_graph -n network.cif -o observations_dir/ --show-repairs 10

For more options you can ask for help as follows:

> opt_graph -h
opt_graph 2.1.0
Sven Thiele <sthiele78@gmail.com>
Opt-graph confronts interaction graph models with observations of (signed) changes between two measured
states. Opt-graph computes networks fitting the observation data by removing (or adding) a minimal number
of edges in the given network.

USAGE:
    opt_graph [FLAGS] [OPTIONS] --network <network-file> --observations <observations-dir>

FLAGS:
    -a, --auto-inputs               Declare nodes with indegree 0 as inputs
        --depmat                    Combine multiple states, a change must be explained by an                                elementary path from an input
        --elempath                  Every change must be explained by an elementary path from an                             input
        --founded-constraints-off   Disable foundedness constraints
        --fwd-propagation-off       Disable forward propagation constraints
    -h, --help                      Prints help information
    -V, --version                   Prints version information

OPTIONS:
    -r, --show-repairs <max-repairs>        Show max-repairs repairs, default is OFF, 0=all
    -n, --network <network-file>            Influence graph in CIF format
    -o, --observations <observations-dir>   Directory of observations in bioquali format
    -m, --repair-mode <repair-mode>         Repair mode: remove = remove edges (default),
                                                       optgraph = add + remove edges,
                                                       flip = flip direction of edges