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sys-bio
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temp-biomodels
Temporary place for coordination of updating existing Biomodels
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SED-ML file points to non-existing model name
#141
maurosilber
closed
1 year ago
1
Put thumbnails in when they work.
#140
luciansmith
opened
1 year ago
0
Add RDF information for biosimulations
#139
luciansmith
opened
1 year ago
0
Alt xppaut
#138
luciansmith
closed
1 year ago
0
Many models cause Tellurium to have a segmentation fault.
#137
joseph-hellerstein
closed
2 years ago
8
feat: add script to submit omex archive to biosimulations
#136
bilalshaikh42
closed
2 years ago
0
Update biomodels
#135
luciansmith
closed
2 years ago
0
'urn' versions added back in official runs, somehow.
#134
luciansmith
closed
2 years ago
1
Which XML to add in the COMBINE archive?
#133
freiburgermsu
closed
2 years ago
13
fix: fixed curation image for BIOMD0000000901
#132
freiburgermsu
closed
2 years ago
2
Fix curation image for 901
#131
luciansmith
closed
2 years ago
2
Parallel GitHub actions
#130
luciansmith
closed
2 years ago
0
Validate images
#129
jonrkarr
closed
2 years ago
0
Fix for new parallelization scheme.
#128
luciansmith
closed
2 years ago
2
Format of curation images is not correctly encoded into the HTML for the BioModels website
#127
jonrkarr
opened
2 years ago
0
Clarify curation notes to elaborate on the associated COPASI tasks(s)
#126
jonrkarr
opened
2 years ago
1
scrape images & curation notes, previous edits to the manual_edits directory
#125
freiburgermsu
closed
2 years ago
2
Remove potentially duplicate SBML file for BIOMD0000000622
#124
jonrkarr
closed
2 years ago
2
SBML versions of the COPASI files and duplicate SED-ML files
#123
freiburgermsu
closed
2 years ago
2
Add validation that files are properly encoded with UTF-8
#122
jonrkarr
opened
2 years ago
0
parallelization of the Actions YAML and the definition of additional …
#121
freiburgermsu
closed
2 years ago
1
curation notes requests script and scraped curation notes
#120
freiburgermsu
closed
2 years ago
0
Bad scripts
#119
freiburgermsu
closed
2 years ago
0
BIOMD0000000561-notebook in BIOMD0000000562
#118
freiburgermsu
opened
2 years ago
0
Fix more issues
#117
luciansmith
closed
2 years ago
0
check all Model PDFs for an error
#116
freiburgermsu
closed
2 years ago
2
Fixes to issues found by latest tests:
#115
luciansmith
closed
2 years ago
1
Deal with KINSOL used as the steady state algorithm.
#114
luciansmith
opened
2 years ago
7
Non parallel branch
#113
luciansmith
closed
2 years ago
0
Pull recent changes.
#112
luciansmith
closed
2 years ago
0
Investigate GitHub actions failures
#111
luciansmith
closed
2 years ago
10
fix: clean up importing plot style from CPS files
#110
jonrkarr
closed
2 years ago
3
Updated Copasi output: 637
#109
luciansmith
closed
2 years ago
6
remove bad SVG & PNG images generated by SBFC
#108
freiburgermsu
closed
2 years ago
2
DRAFT: remove bad SVG & PNG images generated by SBFC
#107
jonrkarr
closed
2 years ago
8
BIOMD0000000585 curation figure
#106
freiburgermsu
closed
2 years ago
0
Detect and correct incorrect encodings
#105
jonrkarr
closed
2 years ago
2
Correct character encoding issues in SED-ML files
#104
jonrkarr
closed
2 years ago
2
Add curators notes and images
#103
jonrkarr
closed
2 years ago
12
Remove bad PNG and SVG files generated by SBFC
#102
jonrkarr
closed
2 years ago
2
Add SED-ML model changes for all possible parameters
#101
jonrkarr
closed
2 years ago
6
Character encoding issues, particular in copied abstracts
#100
luciansmith
closed
2 years ago
8
Ensure exported OWL files are OK
#99
luciansmith
closed
2 years ago
11
Validator: ensure SBFC produced reasonable PDF
#98
luciansmith
closed
2 years ago
14
Validate content of PDFs and remove non-sensical PDFs created by the Systems Biology Format Converter
#97
jonrkarr
closed
2 years ago
3
Delete URN versions of models
#96
jonrkarr
closed
2 years ago
1
Review SED-ML files that purport to reproduce multiple published figures
#95
jonrkarr
opened
3 years ago
1
Correct non-zero SED-ML output start times
#94
jonrkarr
closed
2 years ago
6
Concentration units in curator's notes appear to be off by 10^-3 in BIOMD0000000755
#93
jonrkarr
opened
3 years ago
1
3D, 3E labels are mixed up in curator's image for `BIOMD0000000739`
#92
jonrkarr
opened
3 years ago
0
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