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Translational Informatics Management System (TIMS)

Translational Informatics Management System (TIMS): Towards OMICS based clinical data management for long term curation of clinical studies - Published in JOSS (2019)

https://github.com/bii-absd/tims

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 5 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

TIMS (Translation Informatics Management System) is an software effort by the ABSD (Analytics of Biological Sequence Data) team in the Bioinformatics Institute (BII), Agency of Science, Technology and Research (A*STAR), Singapore.

Basic Info
  • Host: GitHub
  • Owner: bii-absd
  • License: agpl-3.0
  • Language: Java
  • Default Branch: tims_agpl3
  • Size: 49.6 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 1
  • Open Issues: 1
  • Releases: 1
Created almost 7 years ago · Last pushed over 6 years ago
Metadata Files
Readme Contributing License

readme.md

About TIMS - Translational Informatics Management System

TIMS is an OMICS based clinical data management open-source software that curates study-related clinical information, manages the raw processing of diverse OMICS datasets to a preprocessed analysis ready state and finally visualizes the clinical information and processed output in a single access-controlled and audit trailed environment. Most importantly, this data management system provides the skeletal open-source software framework for which any appropriate OMICS pipelines and visualizers can be integrated seamlessly in a scaleable fashion.

Please refer to paper folder for full manuscript.

Trying out TIMS

Minimum System requirements : Intel i7 processor, 32GB of RAM and at least 500GB of storage space on Ubuntu Linux LTS 16.0.4.

  • Via installation : Refer to guide (TIMS-v2.05-Automated-Installation-Guide.pdf) and shell script (TIMS_Installation.sh) in Installation folder.

  • Via Live Demo : Available at https://tims.bii.a-star.edu.sg/TIMS/login.xhtml. Please download the quick guide (TIMS-v2.05-Quick-Start-Guide.pdf) from the Manual & Guide folder for instructions.

TIM Instructions

Please refer to Manual & Guide folder for documentation on TIMS.

Availability of datasets

The datasets used in TIMS documentation are available for download at https://figshare.com/articles/TestData_tar/9083936.

Community guidelines

Please refer to CONTRIBUTING.md.

Owner

  • Login: bii-absd
  • Kind: user

JOSS Publication

Translational Informatics Management System (TIMS): Towards OMICS based clinical data management for long term curation of clinical studies
Published
August 03, 2019
DOI
Volume 4, Issue 40, Page 1533
Authors
Weihong Tay ORCID
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)
Erwin Tantoso ORCID
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)
Frank Eisenhaber ORCID
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)
Wing-Cheong Wong ORCID
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)
Editor
Charlotte Soneson ORCID
Tags
Data management OMICS
View PDF Review Thread Software Archive

GitHub Events

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Last Year

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Last synced: 7 months ago

All Time
  • Total Commits: 871
  • Total Committers: 5
  • Avg Commits per committer: 174.2
  • Development Distribution Score (DDS): 0.255
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Tay Wei Hong w****5@y****g 649
bii-absd a****d@b****g 141
Tay Wei Hong t****h@b****g 79
Daniel S. Katz d****z@i****g 1
Charlotte Soneson c****n@g****m 1
Committer Domains (Top 20 + Academic)
bii.a-star.edu.sg: 2 ieee.org: 1 yahoo.com.sg: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: about 10 hours
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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