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dinkum-bio
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dinkum
very simple cis-regulatory gene regulatory network simulation
GNU Affero General Public License v3.0
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check that genes in display are actually in model
#45
ctb
opened
4 weeks ago
0
simplify/improve receptor/ligand/cofactor stuff.
#44
ctb
opened
4 weeks ago
1
how do we support big models?
#43
ctb
opened
4 weeks ago
0
provided a weighted or, with both positive and repressive interactions
#42
ctb
opened
4 weeks ago
0
add accumulation curves a la decay curves?
#41
ctb
opened
4 weeks ago
0
add code coverage analysis
#40
ctb
opened
4 weeks ago
0
WIP: run notebooks as part of tests
#39
ctb
opened
1 month ago
0
MRG: fix git history mismatch
#38
ctb
closed
1 month ago
0
can we improve dinkum custom activation classes?
#37
ctb
closed
1 month ago
1
MRG: better custom activation functions, more tests
#36
ctb
closed
1 month ago
0
integrate GERN notebooks better
#35
ctb
opened
1 month ago
0
MRG: update `.gitignore` to include `.DS_Store`
#34
ctb
closed
1 month ago
0
improve dinkum exceptions
#33
ctb
opened
1 month ago
0
check on delays - good? > 0, < ...
#32
ctb
opened
1 month ago
0
lock down/validate inputs to arbitrary functions
#31
ctb
opened
1 month ago
0
complain if existing gene in new rule when adding
#30
ctb
opened
1 month ago
0
support tissues -> btp export
#29
ctb
opened
1 month ago
0
support indirect/hypothetical/dotted lines; more generally, support annotation of connections.
#28
ctb
opened
1 month ago
0
MRG: add script to output a BioTapestry csv from a dinkum model
#27
ctb
closed
1 month ago
0
MRG: fix version: 0.4.0
#26
ctb
closed
1 month ago
0
different colors for different types of genes?
#25
ctb
opened
1 month ago
1
design principles
#24
ctb
opened
1 month ago
1
MRG: split into present w/levels, and active
#23
ctb
closed
1 month ago
0
MRG: fix tissue display when there's more than 2 tissues; bump to v0.3.4.
#22
ctb
closed
1 month ago
0
change states to relative time rather than absolute time, for functions
#21
ctb
opened
1 month ago
0
MRG: update `run_and_display` fn and API; bump to 0.3.3
#20
ctb
closed
1 month ago
0
MRG: fix ligands; move `is_present` to be an interaction
#19
ctb
closed
1 month ago
0
remove old ligand stuff after GERN 2024
#18
ctb
opened
1 month ago
0
MRG: cleanup, refactor, and merge ligand changes; v0.3.1
#17
ctb
closed
1 month ago
1
MRG: further update to ligand behavior
#16
ctb
closed
1 month ago
0
MRG: upgrades to v0.3
#15
ctb
closed
1 month ago
0
new version/release considerations:
#14
ctb
opened
1 month ago
0
MRG: minor Makefile and README updates
#13
ctb
closed
1 month ago
0
consider renaming to fair-dinkum?
#12
ctb
opened
1 month ago
0
MRG: rename to dinkum-bio
#11
ctb
closed
1 month ago
0
MRG: Prep for GERN 2024 ;).
#10
ctb
closed
1 month ago
0
WIP: add notebook for experimenting with gene drawings
#9
ctb
opened
12 months ago
0
MRG: refactor states to allow for arbitrary timepoint checking; add delay
#8
ctb
closed
12 months ago
0
MRG: update `Timecourse` to run everything, and store by timepoint
#7
ctb
closed
1 year ago
0
MRG: misc cleanup & feature add
#6
ctb
closed
1 year ago
0
MRG: generalize drawing to use both Pillow and ipycanvas
#5
ctb
closed
1 year ago
0
MRG: add notebook to docs
#4
ctb
closed
1 year ago
0
MRG: add ipywidgets to dependencies
#3
ctb
closed
1 year ago
0
MRG: add basic drawing notebook etc.
#2
ctb
closed
1 year ago
0
MRG: initial functionality
#1
ctb
closed
1 year ago
0