Flask API to facilitate communication between SBOLCanvas and iBioSim
To create the Docker container, navigate to the bioSimPortal directory on your machine and run:
docker build . -t biosimportal
Once the build is finished, run:
docker run -p 5000:5000 biosimportal
Now HTTP requests can be sent to localhost:5000
When sending a POST request to the app, parameters for simulation or conversion are required in the query parameters of the request. Without these parameters, iBioSim won't have any arguments to run the conversion or analysis jar files with, so it will likely error out (with the exception of running analysis on a COMBINE Archive).
In Postman, attach a COMBINE Archive with a .zip extension to the body of the request, and send the request to:
http://localhost:5000/analyze
Attach the SBML file ending with 'topModule.xml' to the body of the request, and put the following in the request field:
http://localhost:5000/analyze
Then under the Params tab using the Key-Value Edit, add (at minimum) arguments for the simulation type, number of runs, and time limit for the simulation.
Argument Keys and Values should be in the following form:
| Key Name | Value | Description | Corresponding Flag |
|---|---|---|---|
| directory | path-to-project-directory | project directory | -d |
| properties | path-to-properties-file | loads a properties file | -p |
| init_time | number (usually 0) | non-negative double initial simulation time | -ti |
| lim_time | number | non-negative double simulation time limit | -tl |
| out_time | number | non-negative double output time | -ot |
| print_interval | number | positive double for print interval | -pi |
| min_step | number | positive double for minimum step time | -m0 |
| max_step | number | positive double for maximum step time | -m1 |
| abs_err | number | positive double for absolute error | -aErr |
| rel_err | number | positive double for relative error | -sErr |
| seed | number | long for random seed | -sd |
| runs | number | positive integer for number of runs | -r |
| simulation | ode, hode, ssa, hssa, dfba, jode, jssa. | simulation type | -sim |
- Note: any paths in either the 'directory' or 'properties' values should have every "/" replaced with "-".
Attach the file to be converted in the body of the request, and put the following in the request field:
http://localhost:5000/convert
Argument Keys and Values should be in the following form:
| Key Name | Value | Description | Corresponding Flag |
|---|---|---|---|
| best_practices | (leave empty) | check best practices | -b |
| results_file | (leave empty) | the name of the file that will be produced to hold the result of the second SBOL file, if SBOL file diff was selected | -cf |
| display_error_trace | (leave empty) | display detailed error trace | -d |
| second_SBOL_file | (leave empty) | the second SBOL file to compare to the main SBOL file | -e |
| export_single_file | (leave empty) | export SBML hierarchical models in a single output file | -esf |
| cont_first_error | (leave empty) | continue after first error | -f |
| allow_incomplete | (leave empty) | allow SBOL document to be incomplete | -i |
| language | SBOL1, SBOL2, GenBank, FASTA, SBML | specifies language for output (default=SBOL2). To output FASTA or GenBank, no SBOL default URI prefix is needed. | -l |
| main_file_name | file_name.xml | The name of the file that will be produced to hold the result of the main SBOL file, if SBOL file diff was selected | -mf |
| allow_noncompliant_uri | (leave empty) | allow non-compliant URIs | -n |
| no_output | (leave empty) | indicate no output file to be generated from validation. Instead, print result to console/command line. | -no |
| prefix | <URIPrefix> |
default URI prefix to set an SBOLDocument | -p |
| sbml_ref | full-path-to-SBML | The full path of external SBML files to be referenced in the SBML2SBOL conversion | -rsbml |
| sbol_ref | full-path-to-SBOL | The full path of external SBOL files to be referenced in the SBML2SBOL conversion | -rsbol |
| select | <topLevelURI> |
select only this object and those it references | -s |
| types_in_uri | (leave empty) | uses types in URIs | -t |
| mark_version | number | mark version of data objects created during conversion | -v |
| repository | "https://www.link-to-repository.dummy" | The specified synbiohub repository the user wants VPR model generator to connect to | -r |
| environment | full-path-to-SBML-env-file | is the complete directory path of the environmental file to instantiate to your model. This only works when VPR model generator is used | -env |
| cello | (leave empty) | This option is for dynamic modeling of Cello parts and parametrization | -Cello |
- Note: When the value of an argument's field is left blank, that key should still be checked if it needs to be included in the request.
Attach the SBOL file in the body of the request, and put the following in the request field:
http://localhost:5000/convert_and_simulate
Argument key-value pairs follow the previously specified formats. Any and all arguments for conversion or analysis go into the query for this request.
A Download plugin for SynBioHub using the iBioSim Server API. The plugin has 3 endpoints status, evaluate, and run. A public instance of the iBioSim server is located at https://ibiosim.synbiohub.org.
The status endpoint is located at https://ibiosim.synbiohub.org/status. SynBioHub sends a status request to the status endpoint, the plugin returns a conformation if active and running. The endpoint can be accessed using a web browser or an application like Postman using a GET request.
The evaluate request tests whether the plugin can handle the data that SynBioHub wishes to send. For the iBioSim plugin the data type has to be collection.
The endpoint can be reached at https://ibiosim.synbiohub.org/evaluate and checked by Postman using a POST request with the following body:
{"type": "Collection"}
SynBioHub sends the data to the run endpoint and downloads the final results of the simulated .omex file as a .png.
The endpoint can be reached at https://ibiosim.synbiohub.org/run and checked by Postman using a POST request with an example body like followed:
{ "instanceUrl": "https://synbiohub.org/", "complete_sbol": "https://synbiohub.org/public/iGEM_2016_interlab/iGEM_2016_interlab_collection/1/sbol", "genbank": "https://synbiohub.org/public/iGEM_2016_interlab/iGEM_2016_interlab_collection/1/gb", "top_level": "https://synbiohub.org/public/iGEM_2016_interlab/iGEM_2016_interlab_collection/1", "size": 7, "type": "Collection", "shallow_sbol": "https://synbiohub.org/public/iGEM_2016_interlab/iGEM_2016_interlab_collection/1/sbolnr" }
Please make sure to make the according changes to the instanceUrl, complete_sbol, etc.
To install an image of the plug-in locally run docker pull synbiohub/plugin-download-ibiosim:snapshot. Run the plugin with docker run -p 8080:5000 synbiohub/plugin-download-ibiosim:snapshot. Check it is up using localhost:8080.