karrlab / datanator Goto Github PK

To address https://karrlab.slack.com/archives/DMX3JM9TM/p1590409919003000

• Remove datanator.api module
• Update h1_hesc to use a specific commit of datanator

Protein half-life
protein modifications
metablome
rna abundance
rna half-life
rna modifications

Limit Groups to ones existing in current "uniprot" collection.
example link

The == constraint for urllib3 in requirements.txt was creating problems for the installation of datanator in CircleCI. I converted it to a >= constraint, which is more flexible. Everything seems to be fine. Is there a reason why you need a specific version?

The same question applies to datanator_query_python (pytz).

See issue #59 from datanator_rest_api

Add a plain text description of the CC BY-NC-ND license to the quilt data package at the path LICENSE within the package.

The file can be copied from here: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode.txt

I will add more details shortly

• http://www.rna-society.org/rnalocate/
  • Download
  • Article: RNALocate: a resource for RNA subcellular localizations (10.1093/nar/gkw728)
• http://lncatlas.crg.eu/
  • Download
  • Article: LncATLAS database for subcellular localization of long noncoding RNAs (10.1261/rna.060814.117)
• Table S3 of Atlas of Subcellular RNA Localization Revealed by APEX-Seq
  (10.1016/j.cell.2019.05.027)

In the GitHub settings for the repo, archive the repo

KarrLab/datanator_frontend#227 (comment)

Also need to identify the reason for their existence.

KarrLab/datanator_rest_api#85 (comment)

Use x.children to parse out ncbi id and species name.

• Page 8 of Supplementary text of Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli (10.1074/jbc.M109.095570)

build ec collection, store cofactor info

KarrLab/datanator_rest_api#64 (comment)

These were the start of integration with SBML

Update h1_hesc as needed by making it use a specific old commit of datanator

See wc-env-manager issue #18.

{'_id': ObjectId('5db0d03c69ee2a78fc9e0154')}

KarrLab/datanator_rest_api#114

http://bkms-react.tu-bs.de/download/Reactions_BKMS.tar.gz

Used for test branches of datanator_rest_api and datanator_frontend

Hash the name of reactants without inchikey in [reactants].
KarrLab/datanator_rest_api#91

Hi,

I'm currently working on upgrading my parser for the BRENDA flat file download. I've implemented a few SQLAlchemy models that seemed fitting for the content. Is there any interest on your side in the content of BRENDA?

Facilitate multi-indices aggregation (experimental) to resolve KarrLab/datanator_rest_api#81 (comment)

Kinetic constants in ec collection were parsed from BRENDA. This issue resolves KarrLab/datanator_rest_api#57 automatically when done.

• Remove postgres from code
• Remove postgres config from datanator/config/config.py
• Remove postgres_service from docker_compose.yml
• Remove migrations directory
• Remove manage.py
• Remove postgres from .circleci/config.yml

See issue #55 in datanator_rest_api

• Delete .config

I got the build running again by converting the == requirement constraint for urllib3 to a >= constraint. There are now 11 test failures. See https://circleci.com/gh/KarrLab/datanator/2239.

Addressing issue KarrLab/datanator_rest_api#81 (comment)

Calibrate or re-calibrate a kinetic model of a mammalian signaling pathway

First, find an appropriate model from the curated portion of BioModels

• Represents Homo sapiens or Mus musculus
• Represents a signaling pathway
• Species are annotated with UniProt ids

Here's the SBML files for the curated portion of BioModels.

Second, try to use the PAXdb data either to

• (a) Calibrate the initial species concentrations (i.e., predict the values in the SBML file; the values in the SBML file would serve as the "gold" standard)
• (b) Re-calibrate the initial species concentrations to represent a different organism or cell type

Enhanced Yeast FBA model

Any version could be used as a starting point.

• https://github.com/SysBioChalmers/yeast-GEM
• v8: https://doi.org/10.1038/s41467-019-11581-3
• v7: https://doi.org/10.1089/ind.2013.0013
• v6: https://doi.org/10.1093/database/bat059
• v5: https://doi.org/10.1186/1752-0509-6-55
• v4: https://doi.org/10.1186/1752-0509-4-145
• v3: There is no model labeled v3
• v2: There is no model labeled v2
• v1: https://doi.org/10.1038/nbt1492

Ways to improve the yeast model

• Additional flux constraints equal to {k_cat} * {enzyme abundance}
• More detailed biomass reconstruction using metabolite concentrations from YMBD

Potential ways to demonstrate improvement of the FBA model

• Increase in the number of reactions with non-zero predicted flux
• Increase in the number of exchanged metabolites (metabolites imported from the extracellular media)
• Improved prediction of gene essentiality (would be due to more detailed biomass)
• Resolution of any problem with the original model described in one of the original publications
• Prediction of distribution of growth rates of single cells (demonstrates improvement in capabilities rather than in biological validity)

KarrLab/datanator_rest_api#110

I will add more details shortly