GRAPES-DD is a modified version of GRAPES (available at https://github.com/InfOmics/GRAPES ) in which the trie indexing structure has been replaced with a multi-terminal multiway decision diagram (MTMDD).
GRAPES-DD research paper has been published on BMC Bioinformatics: it is available here.
GRAPES-DD is developed in C++ under GNU\Linux using POSIX Threads programming. It requires the MEDDLY Library 0.15.1 available at https://github.com/asminer/meddly/releases
The GRAPES-DD workflow is composed by two main phases:
- the indexing building phase in which an MTMDD indexing the collection of target graphs is created;
- the filtering phase in which, given a query graph, the set of target graphs is potentially restricted to those sub-graphs probably containing the query.
The GRAPES-DD verification phase remains as in the original version of the software.
We provide all the graphs used during testing.
The directory example/graphs provides the collections of graphs.
The directory example/queries provides both the collections of graphs and the query graphs.
Inside these directory there are two subdirectories:
biochemicaldirectory contains the biochemical graphs: PDBS, PCM and PPI, as well as the single PPI networks (C. elegans, D. melanogaster, H. sapiens, M. musculus and S. cerevisiae).syntheticdirectory contains the synthetic Barabasi and Forestfire graphs.- Barabasi folder structure is the following:
Barabasi/directed/num_nodes/degree/target-powerP-ID_LabelRange.gfdwhere:- num_nodes is the number of vertices of the graph
- degree is the average degree of a vertex
- P is the exponent of the power-law
- LabelRange is the percentage of distinct labels respect to the number of vertices.
- ForestFire folder structure is the following:
ForestFire/directed/num_nodes/p/targetID_LabelRange.gfdwhere:- num_nodes is the number of vertices of the graph
- p is the probability of a link between two vertices
- LabelRange is the percentage of distinct labels respect to the numer of vertices.
- Barabasi folder structure is the following:
Each target graph presents in the queries folder has a dedicated subfolder containing the query graphs extracted from it. Query folder names represent the number of vertices of the query graph. Query graph names are LabelRange_sub_ID.gfd.
GRAPES-DD is developed in C++ under GNU\Linux using POSIX Threads programming. It requires the MEDDLY Library 0.15.1 available at https://github.com/asminer/meddly/releases
The executable grapes_dd allows you to both build the database index and to run a query.
You can try and compare GRAPES-DD and GRAPES performances by using the runTest.py python script. Tests will be run through Docker if it is installed.
Index building phase:
./runTest.py [-i folder_database/graph_database.gfd] -l lp -t num_threads
Index building + query matching phase:
./runTest.py [-i folder_database/graph_database.gfd -q folder_database/folder_query/query_graph.gff] -l lp -t nt
| Parameter | Description |
|---|---|
| -i db_file | path of the textual graphs database file |
| -q query_file | path of the textual graph query file |
| -l lp | specify feature paths length, namely the depth of the DFS which extract paths. lp must be greather than 1, eg -lp 3. Default value is 4. |
| -t nt | number of threads to be used during matching phase. Default value is 1. |
We recommend you to run the software via Docker. See https://www.docker.com/
ATTENTION: the query graph file must be located in a subdirectory of the graph database file. Query graphs are graph database specific.
Executables are available only after building source code on your system. Use the build_all.sh script to build the grapes_dd executable.
./build_all.sh
Build the index of the given database of graphs.
./grapes_dd -i db_file -l lp -d bool
| Parameter | Description |
|---|---|
| -i db_file | textual graphs database file |
| -l lp | specify feature paths length, namely the depth of the DFS which extract paths. lp must be greather than 1, eg -lp 3. Default value is 4. |
| -d bool | flag indicating if the graphs are directed (true) or undirected (false). Default value is true. |
The indexing phase produces the db_file.index.lp.mtdd file in which the database index is stored.
./grapes_dd -i db_file -q query_file -l lp -d bool -t nthreads
| Attribute | Description |
|---|---|
| -i db_file | textual graphs database file |
| -q query_file | textual query graph file. It must contain just one graph |
| -l lp | specify feature paths length, namely the depth of the DFS which extract paths. lp must be greather than 1, eg -lp 3. Default value is 4. |
| -d bool | flag indicating if the graphs are directed (true) or undirected (false). Default value is true. |
| -t nthreads | number of threads to be used during matching phase |
ATTENTION: before run a query, the database index must have been computed and the resultant file must be maintained in the same directory of the database textual file.
We built a Docker image containing both GRAPES-DD and GRAPES. In the folder where the Dockerfile is located, run the following command to build the image:
docker build -t "grapes_dd" .
You have to mount the folder containing the graph database in /data/db_folder.
docker run -v db_folder:/data/db_file grapes_dd [mode] -i db_file -l lp -d bool
| Parameter | Description |
|---|---|
| mode | specify the tool to be used (grapes or grapes_dd). |
| -i db_file | textual graphs database file |
| -l lp | specify feature paths length, namely the depth of the DFS which extract paths. lp must be greather than 1, eg -lp 3. Default value is 4. |
| -d bool | flag indicating if the graphs are directed (true) or undirected (false). Default value is true. |
You have to mount the folders containing the graph database and the query file in /data/db_file and /data/query_file, respectively.
docker run -v db_folder:/data/db_file -v query_folder:/data/query_file grapes_dd [grapes|grapes_dd] -i db_file -l lp -d bool -t nthreads
| Parameter | Description |
|---|---|
| mode | specify the tool to be used (grapes or grapes_dd). |
| -i db_file | textual graphs database file |
| -q query_file | textual query graph file. It must contain just one graph |
| -l lp | specify feature paths length, namely the depth of the DFS which extract paths. lp must be greather than 1, eg -lp 3. Default value is 4. |
| -d bool | flag indicating if the graphs are directed (true) or undirected (false). Default value is true. |
| -t nthreads | number of threads to be used during matching phase |