https://github.com/alleninstitute/bcdc-dashboards

Science Score: 13.0%

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
○
DOI references
○
Academic publication links
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (7.9%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: AllenInstitute
Language: Jupyter Notebook
Default Branch: master
Size: 2.57 MB

Statistics

Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Created over 3 years ago · Last pushed almost 3 years ago

Metadata Files

Readme

BCDC-Dashboards

This repository is intended to store the codes for the BICAN dashboard, which takes the BCDC-Metadata repository as the input, performs data wrangling and launches the dashboard app script. The current version is a demo version that lives in the local environment and has not been integrated with the other pipelines yet, hence, the code structures are subject to change once the integration with the rest of the existing pipelines (i.e. databases, ontologies) happens.

Installation

Please see the Dev branch for instructions

Workflow

Input: BCDC-Metadata
Data Wrangling: dashboarddatawrangling.ipynb Output: dashcountdf.csv
Dashboard script: testtabs.py (takes dashcount_df.csv as input) Output: Dashboard page with visualizations

Business logics:

The current dashboard allows the views of specimen counts, data depositions, and donor/subject counts by different categories. Detailed categories can be viewed in the dictionary file.

While counting, the groups and categories will be collapsed into similar terminologies to reduce the complexity of the plots so that they are more readable, and the grouping will be done primarily for sample types, specimen types, species, techniques, and modalities. It is expected that this pipeline will be connected with external taxonomy/ontology hierarchies to determine the most interoperable way of collapsing the terminologies.

dashboardlogiccomponents.pdf

There are three panels in the dashboard: 1. Specimen counts by modality: a. For 'imaging' and 'anatomy', count the number of brains and tissues samples processed. b. For OMICs data, count the number of cells and libraries processed. c. For neuron reconstructions, count the number of cells reconstructed. d. For multimodals, count the number of cells processed.

Owner

Name: Allen Institute
Login: AllenInstitute
Kind: organization
Location: Seattle, WA

Website: https://alleninstitute.org
Repositories: 184
Profile: https://github.com/AllenInstitute

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total

Last Year

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 0
Total pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 25 days
Total issue authors: 0
Total pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 2.0
Merged pull requests: 0
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

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science