pypath
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saezlab
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
At some point we should run `cProfile` for all the main database classes and also the `utils.mapping`. Also we should inspect the memory usage. We should take care especially about...
Add a database (tsv, json or sqlite) to the cache where we maintain a record of the last download date and the URL of each file in the cache. The...
A Dockerfile would be really useful to provide so the entire database could be built from scratch (all dependencies, resources, etc.)
At the momet the log is too verbose. A verbosity level should be assigned to each log message, which is the second argument of the `_log` method, e.g. `self._log('message', 1)`....
We process PhosphoSite from two sources: the tabular and the BioPax. The former does not contain references, the latter we don't extract the PTMs from. We should use only the...
Our team [EMBL-EBI/BioModels] has a trainee who is using your modules in her experiments. We are having a chance to work together to push the work forward. What we have...
-- The pre-processing of network data should be organized in a separate module. -- Here we should have classes which are responsible for processing an entire dataset, one line and...
Hi, CellphoneDB recently released version v4 of its database and I was wondering if it will be included into the consensus resource of LIANA anytime soon. I'm very interested in...
There should be an async option since some API request take long to respond and we may have 14000 more requests to make which is a real case in KEGG...
