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sorgerlab
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indra
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
http://indra.bio
BSD 2-Clause "Simplified" License
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Add fix for issue with latest SIGNOR release
#1453
bgyori
closed
1 week ago
0
Update Flask, Flask Restx, unpin Gilda
#1452
kkaris
opened
2 weeks ago
1
Documentation fixes
#1451
bgyori
closed
3 weeks ago
0
Processor improvements
#1450
bgyori
closed
4 weeks ago
0
Add client for RGD database
#1449
bgyori
closed
1 month ago
0
Flask>=3 requires changes to flask-jwt-extended usage
#1448
kkaris
opened
1 month ago
0
Networkx 3 compatibility
#1447
kkaris
closed
1 month ago
0
Replace inspect.getargspec with inspect.getfullargspec
#1446
kkaris
opened
1 month ago
1
Replace `inspect.getargspec` with `inspect.getfullargspec` (or possibly `inspect.signature`)
#1445
kkaris
closed
1 month ago
0
Access Biopax
#1444
Siliegia
opened
1 month ago
2
Extend to Python 3.12 compatibility
#1443
bgyori
closed
2 months ago
0
Remove networkx<3 version constraint
#1442
bgyori
closed
1 month ago
2
Remove pandas version restriction
#1441
bgyori
closed
2 months ago
0
Move markupsafe version constraint
#1440
bgyori
closed
3 months ago
0
Implement completing source counts in HTML assembler
#1439
bgyori
closed
3 months ago
0
Having problem with Python 3.12 at macOS
#1438
muhammadshoaib
opened
5 months ago
3
Remove lib2to3 logging patch
#1437
bgyori
closed
5 months ago
0
Update resource files
#1436
bgyori
closed
5 months ago
0
Reimplement cBioPortal client for new API
#1435
bgyori
closed
5 months ago
0
cBioPortal legacy API is shut down
#1434
kkaris
closed
2 months ago
2
Remove mesh cycle from bio-ontology
#1433
kkaris
closed
6 months ago
1
Add version to file docstring and log message in bio ontology CLI
#1432
kkaris
closed
6 months ago
0
Update MeSH to 2024
#1431
bgyori
closed
6 months ago
0
Improve PubMed metadata extraction handling
#1430
bgyori
closed
6 months ago
0
Add Ensembl info for MGI genes
#1429
bgyori
closed
7 months ago
0
Pubmed retractions
#1428
kkaris
closed
6 months ago
0
Add article retraction resource, functionality for filtering on article type tags
#1427
kkaris
closed
6 months ago
1
Add more robust retry to the pubmed client's send_request
#1426
kkaris
closed
7 months ago
2
Use RTD config for docs build
#1425
bgyori
closed
8 months ago
0
Implement retrieving more than 10k PMIDs and all metadata
#1424
bgyori
closed
7 months ago
0
Db sources updates
#1423
kkaris
closed
7 months ago
0
RLIMS-P invalid statement error
#1422
kkaris
closed
7 months ago
2
HPRD is now behind login, server responds with 500
#1421
kkaris
closed
10 months ago
1
CausalBioNet processing - KeyError while processing jgif file
#1420
kkaris
closed
7 months ago
3
Signor processor error
#1419
kkaris
closed
7 months ago
2
Ubibrowser KeyError
#1418
kkaris
closed
7 months ago
3
Update dependencies
#1417
bgyori
closed
10 months ago
0
Journal info
#1416
kkaris
closed
10 months ago
4
Update HGNC resource
#1415
bgyori
closed
1 year ago
0
Handle underscores in agent IDs for DB query
#1414
bgyori
closed
1 year ago
0
PubMed XML save option
#1413
bgyori
closed
1 year ago
0
Add coordinate info to Agent extraction endpoints from readers
#1412
bgyori
closed
1 year ago
0
Standardize MeSH 2022
#1411
cthoyt
closed
6 months ago
0
Add Python 3.10 testing
#1410
bgyori
closed
1 year ago
0
Update SIGNOR processor and FamPlex
#1409
bgyori
closed
1 year ago
0
Update documentation
#1408
cthoyt
closed
1 year ago
0
Get article references, either just PMIDs or details
#1407
pagreene
closed
1 year ago
0
Allow enhanced author parsing
#1406
pagreene
closed
1 year ago
0
Migrate testing from nosetests to pytest
#1405
bgyori
closed
1 year ago
0
Python and pandas compatibility adjustments
#1404
bgyori
closed
1 year ago
0
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