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Hello again,
I'm using your program and it is awesome!
I do have one suggestion, that I think may help many CG users. That is adding the restricted bending angle potential (gromacs function 10)…
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I am trying to plot some genes using data level 4 for my compound (BRD-K55591206) on HepG2 cells.
There are two signatures with HepG2 cells at level 5:
LJP008_HEPG2_24H:J01
POL001_HEPG2_24H:J09
…
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for logs in /var/log/httpd/lincs.hms.harvard.edu:
- set log levels
- direct non-essential logging output to file
- apply changes on dev as well
@jmuhlich
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I think the full list of Globus groups is:
CFDE-Portal-Curator
CFDE-Portal-Admin
CFDE-Portal-Reviewers
NIH CFDE 4DN Approvers
NIH CFDE 4DN Reviewers
NIH CFDE 4DN Submitters
NIH CFDE ExRNA App…
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in train.py, it says de_genes is keyed on cell_drug_dose_comb
```
# genes for every cell_drug_dose combination.
bool_de = dataset.var_names.isin(
np.array(dataset.de_ge…
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In #73 @michaelbornholdt fixed the workflow diagram for processing the LINCS cell painting profiles.
We have since realized that this workflow diagram is incorrect.
@michaelbornholdt - are you a…
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Not really an issue, just a question I couldn't find the answer to in the docs.
What nomenclature or ontology is used to name compounds in the CMap and LINCS L1000 PharmacoSets and perturbation sig…
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cc @shntnu @MarziehHaghighi
Here is list of materials to generate and questions to explore. Please add anything else you think might be useful to check to this list by directly editing my comment:…
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Liz writes:
datasets are not sorting properly by ID # by default. An example is if you do a search within datasets for “kinativ” (http://lincs.hms.harvard.edu/db/datasets/?search=kinativ&extra_form_s…
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So there is a nice test for checking that input id are in the reference list. If an id isn't in the ref list, you get the message "ERROR: requested input id {line} not found in ref_id_list" but the co…