!pip install dash

Requirement already satisfied: dash in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (2.18.1)
Requirement already satisfied: Flask<3.1,>=1.0.4 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (3.0.3)
Requirement already satisfied: Werkzeug<3.1 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (3.0.6)
Requirement already satisfied: plotly>=5.0.0 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (5.24.1)
Requirement already satisfied: dash-html-components==2.0.0 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (2.0.0)
Requirement already satisfied: dash-core-components==2.0.0 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (2.0.0)
Requirement already satisfied: dash-table==5.0.0 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (5.0.0)
Requirement already satisfied: importlib-metadata in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (8.7.0)
Requirement already satisfied: typing-extensions>=4.1.1 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (4.15.0)
Requirement already satisfied: requests in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (2.32.5)
Requirement already satisfied: retrying in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (1.4.2)
Requirement already satisfied: nest-asyncio in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (1.6.0)
Requirement already satisfied: setuptools in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from dash) (80.9.0)
Requirement already satisfied: Jinja2>=3.1.2 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from Flask<3.1,>=1.0.4->dash) (3.1.6)
Requirement already satisfied: itsdangerous>=2.1.2 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from Flask<3.1,>=1.0.4->dash) (2.2.0)
Requirement already satisfied: click>=8.1.3 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from Flask<3.1,>=1.0.4->dash) (8.3.1)
Requirement already satisfied: blinker>=1.6.2 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from Flask<3.1,>=1.0.4->dash) (1.9.0)
Requirement already satisfied: MarkupSafe>=2.1.1 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from Werkzeug<3.1->dash) (3.0.3)
Requirement already satisfied: tenacity>=6.2.0 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from plotly>=5.0.0->dash) (9.1.2)
Requirement already satisfied: packaging in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from plotly>=5.0.0->dash) (25.0)
Requirement already satisfied: zipp>=3.20 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from importlib-metadata->dash) (3.23.0)
Requirement already satisfied: charset_normalizer<4,>=2 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from requests->dash) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from requests->dash) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from requests->dash) (2.5.0)
Requirement already satisfied: certifi>=2017.4.17 in /Users/Roberto/miniforge3/envs/ga4gh/lib/python3.13/site-packages (from requests->dash) (2025.11.12)

import requests
import json
import dash
from typing import List, Optional, Dict, Any
from dash import Dash, dcc, html, Input, Output, callback, dash_table, jupyter_dash
from dash.dependencies import Input, Output
import plotly.express as px
import plotly.graph_objects as go
from plotly.subplots import make_subplots
import pandas as pd
from collections import Counter
from datetime import datetime
import numpy as np

# Base URL
BASE_URL = "http://analytics-staging.ga4gh.org:8000"

# Github Endpoints
REPO_ENDPOINT = f"{BASE_URL}/github/name/" # fetches repo based on repo name parameter provided by user after name/
REPO_OWNER_ENPOINT = f"{BASE_URL}/github/owner/" # fetches repos based on repo owner parameter provided user after owner/
ALL_REPOS_ENDPOINT = f"{BASE_URL}/github/all"

# PyPi Endpoints
TOTAL_PACKAGES_ENDPOINT = f"{BASE_URL}/pypi/total-packages"
PACKAGE_VERSIONS_ENDPOINT = f"{BASE_URL}/pypi/package-versions"
RELEASES_OVER_YEARS_ENDPOINT = f"{BASE_URL}/pypi/releases-over-years"
PYPI_DETAILS_ENDPOINT = f"{BASE_URL}/pypi/project-details"
FIRST_RELEASES_ENDPOINT = f"{BASE_URL}/pypi/first-releases"
ALL_PACKAGES_ENDPOINT = f"{BASE_URL}/pypi/all-packages"

# PubMed Endpoints
PM_KEYWORD = f"{BASE_URL}/pubmed/articles/GA4GH"

# Function that will take a list of repos and retrieve them from the DB
def get_repos(endpoint: str, list_of_repos: List[str]) -> List[Dict[str, Any]]:

    items: List[Dict[str, Any]] = []
    url = endpoint

    for repo in list_of_repos:
        resp = requests.get(url + repo)
        resp.raise_for_status()
        items.append(resp.json()[0])

    return items

# Function to make a request to the endpoints to return data from the DB addressing any pagination issues
def get_json(endpoint: str, token: Optional[str] = None, per_page: int = 100) -> List[Dict[str, Any]]:

    headers = {}
    if token:
        headers["Authorization"] = f"token {token}"

    params = {"per_page": per_page, "page": 1}
    items: List[Dict[str, Any]] = []
    url = endpoint

    while True:
        resp = requests.get(url, headers=headers, params=params, timeout=30)
        resp.raise_for_status()
        data = resp.json()

        if not isinstance(data, list):
            return data

        items.extend(data)

        if "next" in resp.links:
            url = resp.links["next"]["url"]
            params = None
        else:
            break

    return items


def get_last_year(dates):
    last_year = []
    for d in dates:
        if hasattr(d, "year"):
            y = d.year
        else:
            y = datetime.fromisoformat(d).year
        if y == 2025:
            last_year.append(d)
    return last_year

#PubMed
pubmed_json = get_json(PM_KEYWORD)
pm_df = pd.DataFrame.from_records(pubmed_json)
pm_df['publish_date'] = pd.to_datetime(pm_df['publish_date'], utc=True, errors='raise')
pm_df['year'] = pm_df['publish_date'].dt.year
pm_last_year = get_last_year(pm_df['publish_date'])

# GitHub
GA4GH_json = get_json(ALL_REPOS_ENDPOINT)
gh_df = pd.DataFrame.from_records(GA4GH_json)
gh_df['last_updated'] = pd.to_datetime(gh_df['last_updated'], utc=True, errors='raise')
gh_df['pushed_at'] = pd.to_datetime(gh_df['pushed_at'], utc=True, errors='raise')
gh_df['created_on'] = pd.to_datetime(gh_df['created_on'], utc=True, errors='raise')
gh_last_year = get_last_year(gh_df['created_on'])

# PyPi
pypi_packages_json = get_json(PYPI_DETAILS_ENDPOINT)
pypi_df = pd.DataFrame.from_records(pypi_packages_json)

pypi_first_versions_df = pd.DataFrame.from_records(get_json(FIRST_RELEASES_ENDPOINT))

pypi_df = pypi_df.merge(pypi_first_versions_df,how='inner',on='project_name')
assert pypi_df.shape[0] == int(get_json(TOTAL_PACKAGES_ENDPOINT).get("total_packages", 0))
pypi_df['first_release'] = pd.to_datetime(pypi_df['release_date'], utc=True, errors='raise')

pypi_last_year = get_last_year(pypi_df['first_release'])

def plot_indicators():

    fig = go.Figure()

    fig = make_subplots(
        rows=1, cols=3,
        specs=[[{"type": "indicator"}, {"type": "indicator"}, {"type": "indicator"}]],
        horizontal_spacing=0.08

    )
    fig.add_trace(
        go.Indicator(mode="number+delta", value=pm_df.shape[0], title={"text": "PubMed Articles"}, delta={"reference": pm_df.shape[0] - len(pm_last_year)}),
        row=1, col=3
    )
    fig.add_trace(
        go.Indicator(mode="number+delta", value=gh_df.shape[0], title={"text": "GitHub Repositories"}, delta={"reference": gh_df.shape[0] - len(gh_last_year)}),
        row=1, col=1
    )
    fig.add_trace(
        go.Indicator(mode="number+delta", value=pypi_df.shape[0], title={"text": "PyPi Packages"}, delta={"reference": pypi_df.shape[0] - len(pypi_last_year)}),
        row=1, col=2

    )

    fig.update_layout(
        template="simple_white",
        title={
            "text": "Figure 1: Total GA4GH Data Points Per Source With 2025 Increases\n",
            "x": 0.5,
            "xanchor": "center",
            "font": {"size": 26},
            "pad": {"b": 40},
        },
        margin=dict(l=20, r=20, t=50, b=20),
        height=300,
        width=1000
    )
    fig.show()
plot_indicators()

to_combine_pm_df = pd.DataFrame({'item': pm_df['title'],
                                 'year': pm_df['year'],
                                 'Source': 'PubMed Articles'})

to_combine_gh_df = pd.DataFrame({'item': gh_df['name'],
                                 'year': gh_df['created_on'].dt.year,
                                 'Source': 'GitHub Repos'})

to_combine_pypi_df = pd.DataFrame({'item': pypi_df['project_name'],
                                   'year': pypi_df['first_release'].dt.year,
                                   'Source': 'PyPi Packages'})

combined_year_df = pd.concat([to_combine_pm_df,to_combine_gh_df,to_combine_pypi_df])

# Group by Year and Source
year_plot_df = combined_year_df.groupby(['year', 'Source']).agg({'item': list}).reset_index()
year_plot_df = year_plot_df.sort_values(['Source', 'year'])

# List items and calculate cumulative sum
year_plot_df['items_str'] = year_plot_df['item'].apply(lambda items: '<br>'.join(items))
year_plot_df['yearly_count'] = year_plot_df['item'].apply(len)
year_plot_df['yearly_cumulative_count'] = year_plot_df.groupby(['Source'])['yearly_count'].cumsum()

def plot_year():
    fig = px.line(
        year_plot_df,
        x='year',
        y='yearly_cumulative_count',
        color='Source',
        markers=True,
        title='Figure 2: Growth of GA4GH Resources Over Time',
        labels={'year': 'Year', 'yearly_cumulative_count': 'Total to date'},
        custom_data=['items_str', 'Source', 'yearly_count'],
        template='simple_white'
    )

    # 5. Update Hover Template
    fig.update_traces(
        hovertemplate=(
            '<b>%{customdata[1]}</b><br>' # Source Name
            'Year: %{x}<br>'
            'Number of new items: %{customdata[2]}<br><br>'
            '<b>New Items:</b><br>%{customdata[0]}<extra></extra>'
        ),
        marker=dict(size=8),
    )

    fig.update_layout(
        xaxis_title='Year',
        yaxis_title='Cumulative number of new items',
        title_font_size=26,
        margin=dict(l=40, r=20, t=70, b=120),
        height=600,
        legend_title_text='Resource',
        width=1080
    )
    fig.show()
plot_year()

articles_in_top = []

for j, g in pm_df.groupby('journal'):
    titles_sorted = g.sort_values('title')
    details = "<br>".join(r['title'] for _, r in titles_sorted.iterrows())
    articles_in_top.append({'journal': j, 'Count': len(g), 'Details': details})

top_journals = pd.DataFrame(articles_in_top).sort_values('Count', ascending=False).head(10).reset_index(drop=True)

def plot_top_journals():

    if isinstance(top_journals, pd.Series):
        df = top_journals.reset_index()
        df.columns = ["journal", "Count"]
    else:
        df = top_journals.copy()

    df = df.sort_values("Count", ascending=False).reset_index(drop=True)

    # build customdata for hover (Count + Details if available)
    if "Details" in df.columns:
        customdata = df[["Count", "Details"]].values
        hovertemplate = "Count: %{customdata[0]}<br>%{customdata[1]}<extra></extra>"
    else:
        customdata = df[["Count"]].values
        hovertemplate = "Count: %{customdata[0]}<extra></extra>"

    fig = go.Figure(
        go.Bar(
            x=df["journal"],
            y=df["Count"],
            #marker_color=colors,
            customdata=customdata,
            hovertemplate=hovertemplate,
            marker_line_width=0,

        )
    )

    fig.update_layout(
        title="Figure 3: Top 10 Journals for GA4GH Publications",
        title_font_size=26,
        barmode="relative",
        xaxis_tickangle=-45,
        margin=dict(l=40, r=20, t=80, b=150),
        xaxis_title="Journal",
        yaxis_title="Count",
        legend_title_text=" ",
        height=600,
        template="simple_white",
        width=1000
    )

    fig.show()
plot_top_journals()

fetch_date = '2025-10-01'
target_date = pd.to_datetime(fetch_date, utc=True)

gh_df['days_since_pushed_at'] = (target_date - gh_df['pushed_at']).dt.days
gh_df['days_since_last_updated'] = (target_date - gh_df['last_updated']).dt.days

gh_df['activity_score'] = 1/(1+gh_df['days_since_pushed_at']) + 1/(1+gh_df['days_since_last_updated'])

gh_activity_df = gh_df.sort_values('activity_score', ascending=False).head(15).reset_index(drop=True)

conditions = [
    (gh_df['is_archived'] == False) & (gh_df['days_since_pushed_at'] < 365),
    (gh_df['is_archived'] == False) & (gh_df['days_since_pushed_at'] >= 365) & (gh_df['days_since_pushed_at'] <= 1095),
    (gh_df['is_archived'] == False) & (gh_df['days_since_pushed_at'] > 1095),
    (gh_df['is_archived'] == True)
]
choices = ['Active', 'Moderate activity', 'Inactive', 'Archived']

gh_df['activity_status'] = np.select(conditions, choices, default='Unknown')

gh_activity_counts = gh_df['activity_status'].value_counts().reset_index()
gh_activity_counts.columns = ["Category", "Count"]

def plot_github_status():

    fig = go.Figure(data=[
        go.Pie(
            labels=gh_activity_counts["Category"],
            values=gh_activity_counts["Count"],
            hole=0.4,
            textinfo="label+percent",
            hoverinfo="label+value+percent"
        )
    ])

    fig.update_layout(
        title={
            "text": "Figure 4: Activity Status of the GA4GH GitHub Repositories",
            "x": 0.5,         
            "xanchor": "center",
            "yanchor": "top",
            "font": {"size": 26, "color": "#2C3E50"}
        },
        plot_bgcolor="#f9f9f9",
        legend_title_text='Activity Status',
        paper_bgcolor="#ffffff",
        width=1000,
        height=600
    )

    fig.show()
plot_github_status()

def plot_gh_activity():
    fig = px.bar(
        gh_activity_df,
        x='name',
        y='activity_score',
        labels={'activity_score': 'Count', 'name': 'Repo'},
        title="Figure 5: Most Recently Updated GA4GH-Related Repositories",
        custom_data=['days_since_pushed_at', 'days_since_last_updated'],
    )

    fig.update_traces(
        hovertemplate='Days since last commit: %{customdata[0]}<br>Days since last repo update: %{customdata[1]}<extra></extra>',
        marker_line_width=0
    )

    fig.update_layout(
        barmode='relative',
        xaxis_tickangle=-45,
        margin=dict(l=40, r=20, t=80, b=150),
        xaxis_title='Repository',
        yaxis_title='Recent activity (arbitrary unit)',
        legend_title_text='',
        title_font_size=26,
        height=700,
        width=1000,
        template='simple_white',
    )

    fig.show()

plot_gh_activity()

gh_df['total_interest'] = gh_df['subscribers_count'] + gh_df['stargazers_count'] + gh_df['forks_count']
gh_interest_df = gh_df.sort_values('total_interest', ascending=False).head(10).reset_index(drop=True)

def plot_gh_interest():
    fig = px.bar(
        gh_interest_df,
        x='name',
        y=['subscribers_count','stargazers_count','forks_count'],
        title='Figure 6: Interest Metrics for GA4GH GitHub Repositories',
        color_discrete_sequence=['#540d6e', '#ee4266', '#ffd23f'],
        template='simple_white'
    )

    fig.update_layout(
        barmode='stack',
        xaxis_tickangle=-45,
        margin=dict(l=40, r=20, t=80, b=150),
        xaxis_title='Repository name',
        yaxis_title='Interest (Subscribers + Stargazers + Forks)',
        legend_title_text='Interaction Type',
        title_font_size=26,
        height = 700,
        width=1080
    )

    fig.update_traces(marker_line_width=0)

    fig.show()
plot_gh_interest()

pypi_type_counts = pypi_df['category'].value_counts().reset_index()
pypi_type_counts.columns = ["Category", "Count"]

def plot_pypi_status():

    fig = go.Figure(data=[
        go.Pie(
            labels=pypi_type_counts["Category"],
            values=pypi_type_counts["Count"],
            hole=0.4,
            textinfo="label+percent",
            hoverinfo="label+value+percent"
        )
    ])

    fig.update_layout(
        title={
         "text": "Figure 7: Category of GA4GH-Related PyPi Packages",
            "x": 0.5,         
            "xanchor": "center",
            "yanchor": "top",
            "font": {"size": 26, "color": "#2C3E50"}
        },
        plot_bgcolor="#f9f9f9",
        paper_bgcolor="#ffffff",
        legend_title_text='Category',
        height=600,
        width=1000
    )

    fig.show()
plot_pypi_status()

pypi_all_versions_json = get_json(ALL_PACKAGES_ENDPOINT)

rows_list = []

for ver in pypi_all_versions_json:
    dict1 = {'package': ver['package']['project_name'],
             'package_version': ver['version']['package_version'],
             'release_date': pd.to_datetime(ver['version']['release_date'], utc=True, errors='raise'),
             'category': ver['package']['category']
            }

    rows_list.append(dict1)

pypi_all_versions_df = pd.DataFrame(rows_list)

pypi_all_versions_df = pypi_all_versions_df.sort_values(['package','release_date','category']).reset_index(drop=True)
pypi_release_range_df = pypi_all_versions_df.groupby('package')['release_date'].agg(['first','last','count'])
pypi_release_range_df['range_days'] = (pypi_release_range_df['last']-pypi_release_range_df['first']).dt.days
pypi_release_range_df['frequency_year'] = (pypi_release_range_df['count']/pypi_release_range_df['range_days'])*365
category_per_package = pypi_all_versions_df.groupby('package')['category'].first()
pypi_release_range_df = pypi_release_range_df.join(category_per_package)
pypi_release_range_df['first'] = pypi_release_range_df['first'].dt.strftime('%Y-%m-%d')
pypi_release_range_df['last'] = pypi_release_range_df['last'].dt.strftime('%Y-%m-%d')

pypi_release_range_df = pypi_release_range_df.reset_index()

def plot_pypi_frequency():

    df = (
        pypi_release_range_df[pypi_release_range_df["range_days"] > 90]
        .sort_values("frequency_year", ascending=False)
        .head(10)
        .copy()
    )

    color_map = {
        "Implementation": "#1f77b4",
        "GA4GH Standard": "#2ca02c",
        "Reference": "#ff7f0e",
    }

    colors = df["category"].map(color_map).fillna("#7f7f7f").tolist()

    fig = px.bar(
        df,
        x="package",
        y="frequency_year",
        labels={"frequency_year": "Average number of new versions per year", "package": "Package"},
        title="Figure 8: Most Frequently Released GA4GH-Related PyPi Packages",
        custom_data=["count", "first", "last"],
    )

    fig.update_traces(
        marker_color=colors,
        hovertemplate="%{customdata[0]} versions between %{customdata[1]} and %{customdata[2]}<extra></extra>",
        marker_line_width=0,
    )

    used_cats = [c for c in ["Implementation", "GA4GH Standard", "Reference"] if c in df["category"].unique()]
    for cat in used_cats:
        fig.add_trace(
            go.Scatter(
                x=[None],
                y=[None],
                mode="markers",
                marker=dict(size=10, color=color_map.get(cat, "#7f7f7f")),
                name=cat,
                showlegend=True,
            )
        )

    fig.update_layout(
        barmode="relative",
        xaxis_tickangle=-45,
        margin=dict(l=40, r=200, t=80, b=150),  
        xaxis_title="PyPi package name",
        yaxis_title="Average number of new versions per year",
        legend_title_text="Category",
        legend=dict(orientation="v", x=1.02, y=1),
        height=600,
        width=1080,
        template="simple_white",
         title_font_size=26,
        )

    fig.show()

plot_pypi_frequency()

from IPython.display import display, HTML
total_packages = len(pypi_df)
# Convert DataFrame to HTML with DataTables
col_to_show = ['project_name','description',
               'author_name','author_email','category']

html_str = pypi_df[col_to_show].to_html(classes="display", table_id="my_table", index=False)
html_template = f"""
<h3>Total PyPI Packages: {total_packages}</h3>
{html_str}
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.13.6/css/jquery.dataTables.css">
<script type="text/javascript" charset="utf8" src="https://code.jquery.com/jquery-3.7.1.js"></script>
<script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.js"></script>
<script>
$(document).ready(function() {{
    $('#my_table').DataTable({{
        "pageLength": 10,
        "lengthMenu": [5, 10, 20, 50],
        "order": [[0, "asc"]],
        "searching": true,
        "info": true,
        "paging": true
    }});
}});
</script>
"""
# Display inline in notebook
display(HTML(html_template))

project_name	description	author_name	author_email	category
data-repo-client	Data Repository API	OpenAPI Generator community	team@openapitools.org	Implementation
cwltool	Common workflow language reference implementation	Common workflow language working group	common-workflow-language@googlegroups.com	Implementation
pyphetools	Generate and work with GA4GH phenopackets	None	Peter Robinson <peter.robinson@bih-charite.de>, Daniel Danis <daniel.gordon.danis@protonmail.com>	Implementation
planemo	Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).	None	Galaxy Project and Community <galaxy-committers@lists.galaxyproject.org>	Implementation
bento-lib	A set of common utilities and helpers for Bento platform services.	David Lougheed	david.lougheed@mail.mcgill.ca	Reference
bycon	A Python-based environment for the GA4GH Beacon genomics API	None	Michael Baudis <m@baud.is>	GA4GH Standard
sapporo	The sapporo-service is a standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification.	None	"DDBJ (Bioinfomatics and DDBJ Center)" <tazro.ohta@chiba-u.jp>	Implementation
variation-normalizer	VICC normalization routine for variations	Alex Wagner, Kori Kuzma, James Stevenson	None	Implementation
ga4gh.vrs	GA4GH Variation Representation Specification (VRS) reference implementation	None	Larry Babb <lbabb@broadinstitute.org>, Reece Hart <reecehart@gmail.com>, Andreas Prlic <andreas.prlic@gmail.com>, Alex Wagner <alex.wagner@nationwidechildrens.org>	GA4GH Standard
nmdc-runtime	A runtime system for NMDC data management and orchestration	None	None	Reference
pyega3	EGA python client	EGA team	ega-helpdesk@ebi.ac.uk	Implementation
dnastack-client-library	DNAstack's GA4GH library and CLI	None	DNAstack <devs@dnastack.com>	Implementation
truvari	Structural variant comparison tool for VCFs	None	ACEnglish <acenglish@gmail.com>	Reference
ga4gh.gks.metaschema	GA4GH Genomic Knowledge Standards meta-schema tools	None	Alex Wagner <alex.wagner@nationwidechildrens.org>	GA4GH Standard
ga4gh.vrsatile.pydantic	"Translation of the GA4GH VRS and VRSATILE Schemas to a Pydantic data model"	Alex H. Wagner	alex.wagner@nationwidechildrens.org	Implementation
gpsea	Discover genotype-phenotype correlations with GA4GH phenopackets	None	Lauren Rekerle <lauren.rekerle@jax.org>, Daniel Danis <daniel.danis@bih-charite.de>, Peter Robinson <peter.robinson@bih-charite.de>	Implementation
uta-tools	Service for querying the biocommons.uta database	Wagner Lab, Nationwide Childrens Hospital		Reference
py-tes	Library for communicating with the GA4GH Task Execution API	OHSU Computational Biology	CompBio@ohsu.edu	Implementation
terra-notebook-utils	Utilities for the Terra notebook environment.	Brian Hannafious	bhannafi@ucsc.edu	Implementation
ga4gh	A reference implementation of the GA4GH API	Global Alliance for Genomics and Health	theglobalalliance@genomicsandhealth.org	Implementation
htsget	Python API and command line interface for the GA4GH htsget API.	Jerome Kelleher	jerome.kelleher@well.ox.ac.uk	GA4GH Standard
metakb	A search interface for cancer variant interpretations assembled by aggregating and harmonizing across multiple cancer variant interpretation knowledgebases.	VICC	help@cancervariants.org	Reference
GelReportModels	Genomics England Bioinformatics team model definitions	Bioinformatics Team at Genomics England	antonio.rueda-martin@genomicsengland.co.uk	Implementation
wes-service	GA4GH Workflow Execution Service reference implementation	None	GA4GH Containers and Workflows task team <common-workflow-language@googlegroups.com>	Implementation
refget	Python client for refget	Nathan Sheffield, Michal Stolarczyk	nathan@code.databio.org	GA4GH Standard
candig-server	Server implementation of the CanDIG APIs	CanDIG Team	info@distributedgenomics.ca	Implementation
ga4gh-schemas	GA4GH API Schemas	Global Alliance for Genomics and Health	theglobalalliance@genomicsandhealth.org	Implementation
drsclient	GA4GH DRS Client	CTDS UChicago	cdis@uchicago.edu	Implementation
cgbeacon2	A beacon supporting GA4GH API 1.0	Chiara Rasi	chiara.rasi@scilifelab.se	Implementation
pydantic-tes	Pydantic Models for the GA4GH Task Execution Service	John Chilton	jmchilton@gmail.com	Implementation
vrs-anvil-toolkit	Useful tools and methods for applying GA4GH GKS and VRS models on the NHGRI AnVIL platform.	GKS-AnVIL	None	Implementation
ga4gh-drs-client	Retrieve omics data from Data Repository Service (DRS) web services	Jeremy Adams	jeremy.adams@ga4gh.org	GA4GH Standard
chord-lib	A set of common utilities and helpers for CHORD.	David Lougheed	david.lougheed@mail.mcgill.ca	Implementation
ga4gh.cat-vrs	GA4GH Categorical Variation Representation (Cat-VRS) reference implementation	None	Larry Babb <lbabb@broadinstitute.org>, Alex Wagner <alex.wagner@nationwidechildrens.org>, Daniel Puthawala <daniel.puthawala@nationwidechildrens.org>	GA4GH Standard
phenosentry	A tool and library for quality control and validation of GA4GH Phenopackets.	Michael Gargano	Michael.Gargano@jax.org	Implementation
refget-compliance	A compliance utility reporting system for refget server implementations	Somesh Chaturvedi	somesh.08.96@gmail.com	Implementation
ga4gh.va-spec	GA4GH Variant Annotation (VA) reference implementation	Matt Brush, Javier Lopez	None	GA4GH Standard
ga4gh-client	A client for the GA4GH reference server	Global Alliance for Genomics and Health	theglobalalliance@genomicsandhealth.org	Implementation
fasta-checksum-utils	Library and command-line utility for checksumming FASTA files and individual contigs.	David Lougheed	david.lougheed@gmail.com	Reference
ga4gh-dos-schemas	GA4GH Data Object Service Schemas	Global Alliance for Genomics and Health	theglobalalliance@genomicsandhealth.org	GA4GH Standard
trs-cli	GA4GH TRS Client	ELIXIR Cloud & AAI	sarthakgupta072@gmail.com	Implementation
cwl-tes	Common workflow language reference implementation backended by a GA4GH Task Execution Service	Adam Struck	strucka@ohsu.edu	Implementation
ga4gh-common	Common utilities for GA4GH packages	Global Alliance for Genomics and Health	theglobalalliance@genomicsandhealth.org	Implementation
dcd-mapping	Map MaveDB scoresets to VRS objects	None	Jeremy Arbesfeld <Jeremy.Arbesfeld@nationwidechildrens.org>, James Stevenson <James.Stevenson@nationwidechildrens.org>, Alan Rubin <alan.rubin@wehi.edu.au>, Alex Handler Wagner <Alex.Wagner@nationwidechildrens.org>	Implementation
phenopackets	Phenopacket Schema	None	Michael Gargano <michael.gargano@jax.org>, Daniel Danis <daniel.gordon.danis@protonmail.com>, Jules Jacobsen <j.jacobsen@qmul.ac.uk>, Chris Mungall <cjmungall@lbl.gov>, Peter Robinson <peter.robinson@bih-charite.de>	GA4GH Standard
crypt4gh	GA4GH cryptographic utilities	Frédéric Haziza	frederic.haziza@crg.eu	GA4GH Standard
drs-cli	GA4GH DRS Client	ELIXIR Cloud & AAI	sarthakgupta072@gmail.com	Implementation
ga4gh-testbed-lib	Python library for creating GA4GH testbed reports according to a harmonized, cross-workstream schema	Jeremy Adams	jeremy.adams@ga4gh.org	Implementation
phenopacket-store-toolkit	Collection of GA4GH Phenopackets	None	Daniel Danis <daniel.danis@bih-charite.de>, Peter Robinson <peter.robinson@bih-charite.de>	Implementation
pfb-fhir	Render a PFB graph from FHIR data	bmeg.io	walsbr@ohsu.edu	Reference
sparc-flow	A Python tool to create tools and workflows for processing SPARC datasets in accordance with FAIR principles.	Thiranja Prasad Babarenda Gamage, Chinchien Lin, Jiali Xu, Linkun Gao, Matthew French, Michael Hoffman	None	Reference
jsoncanon	Typed Python implementation of JSON Canonicalization Scheme as described in RFC 8785. Currently lacks full floating point support	Sveinung Gundersen	sveinugu@gmail.com	Implementation
ga4gh-rnaget-compliance	Reports web service compliance to GA4GH RNAget specification	Jeremy Adams	jeremy.adams@ga4gh.org	Implementation
vrsix	Tools for indexing GREGoR VCFs	James Stevenson	None	Implementation
snakemake-executor-plugin-tes	A Snakemake executor plugin for submitting jobs via GA4GH TES.	Sven Twardziok	sven.twardziok@bih-charite.de	Implementation
candig-schemas	CanDIG API Schemas	CanDIG Team	info@distributedgenomics.ca	Implementation
pyEnsemblRest	A Python Ensembl REST API client	Steve Moss	gawbul@gmail.com	Implementation
py-tesseract	Remote code execution with the GA4GH Task Execution API	Adam Struck	strucka@ohsu.edu	Implementation
simple-job-files	Pydantic Models for the GA4GH Task Execution Service	John Chilton	jmchilton@gmail.com	Implementation
ga4ghmongo	A document based Variant database inspired by ga4gh Variants schema	Phelim Bradley	wave@phel.im	Reference
toil-batch-system-tes	A TES batch system plugin for Toil	None	Adam Novak <anovak@soe.ucsc.edu>	Implementation
ga4gh-cli	Console interface for GA4GH-compliant environments	Pavel Nikonorov	info@genxt.network	Implementation
ngstream	Utilities for streaming NGS reads from SRA and GA4GH accessions.	John Didion	github@didion.net	Implementation
rarelink	RareLink - A REDCap-based Python framework linking international registries to HL7 FHIR and GA4GH Phenopackets	None	Adam SL Graefe <adam.graefe@charite.de>, Filip Rehburg <filip.rehburg@charite.de>, Samer Alkarkoukly <mabbouda@uni-koeln.de>, Daniel Danis <daniel.danis@bih-charite.de>, Melissa A Haendel <mhaendel@email.unc.edu>, Peter N Robinson <peter.robinson@bih-charite.de>, Sylvia Thun <sylvia.thun@bih-charite.de>, Oya Beyan <oya.beyan@uni-koeln.de>	Implementation
cgbeacon	Extracts variants from a VCF file and inserts them into a Beacon MySQL database	Chiara Rasi	chiara.rasi@scilifelab.se	Implementation
TEStribute	Task distribution for GA4GH TES instances	ELIXIR Cloud & AAI	alexander.kanitz@alumni.ethz.ch	Implementation
weskit-client	Client for WESkit deployment and workflow execution.	None	Valentin Schneider-Lunitz <valentin.schneider-lunitz@bih-charite.de>	Implementation
tes-client	bravado generated mock GA4GH TES client	ELIXIR Europe	vani11537@one.ducic.ac.in	Implementation
gc-count	None	None	None	Implementation
rd-cdm	An ontology-based rare disease common data model (RD-CDM) harmonising international registries, HL7 FHIR, and GA4GH Phenopackets.	Adam SL Graefe	adam.graefe@charite.de	Implementation
candig-rnaget	A POC implementation of GA4GH RNAGET API	BCGSC	alipski@bcgsc.ca	Implementation
seqrepo-rest-service	SeqRepo REST Service		biocommons contributors <biocommons-dev@googlegroups.com>	Implementation
drs-client	bravado generated mock GA4GH DRS client	ELIXIR Europe	vani11537@one.ducic.ac.in	Implementation
drs-compliance-suite	A compliance utility reporting system for GA4GH DRS server implementations. Supports GA4GH DRS versions - 1.2.0	Yash Puligundla	yasasvini.puligundla@ga4gh.org	Implementation
genophenocorr	Search for genotype-phenotype correlations with GA4GH phenopackets		Lauren Rekerle <lauren.rekerle@jax.org>, Daniel Danis <daniel.danis@jax.org>, Peter Robinson <peter.robinson@jax.org>	Reference
genpei	Implementation of GA4GH WES OpenAPI specification using cwltool.	suecharo	suehiro619@gmail.com	Implementation
ga4gh-phenopacket-core	Python convenience wrappers for Phenopacket Schema	None	Daniel Danis <daniel.gordon.danis@protonmail.com>, Peter Robinson <peter.robinson@bih-charite.de>	GA4GH Standard
vrs-anvil	Commons utilities	Ellrott Lab	None	Implementation
aiva-sample-processor	OpenCRAVAT CSV processor for generating sample CSVs for aiva-database import	Mamidi Health	info@mamidi.co.in	Reference
rnaget-client	A python client to query the RNAget compliant servers	Emilio	righiemilio@gmail.com	Implementation
aiva-vrs	VRS Generator for mapping variants between different Variant Database Tables	Mamidi HealthTech Solutions	info@mamidi.co.in	Implementation
ga4gh-server	A reference implementation of the GA4GH API	Global Alliance for Genomics and Health	theglobalalliance@genomicsandhealth.org	Implementation

Analytics Dashboard Overview¶

How this notebook works¶

How to Run This Notebook on Google Colab (no installation required)¶

Useful information on data sourcing¶

What you can customize¶

How you can contribute¶

What's next on the roadmap¶

Important notes¶

Troubleshooting¶

Setup¶

Libraries required to run this notebook¶

Configurations¶

Figure 1: Total impact¶

Figure 2: Growth of GA4GH resources over time¶

Figure 3: PubMed (Top 10 Journals)¶

Figure 4: Activity status of GA4GH GitHub repositories¶

Figure 5: Most recently updated GA4GH GitHub repositories¶

Figure 6: Interest metrics for GA4GH Github repositories¶

Total PyPI Packages: 82

Analytics Dashboard Overview¶

How this notebook works¶

How to Run This Notebook on Google Colab (no installation required)¶

Useful information on data sourcing¶

What you can customize¶

How you can contribute¶

What's next on the roadmap¶

Important notes¶

Troubleshooting¶

Setup¶

Libraries required to run this notebook¶

Configurations¶

Figure 1: Total impact¶

Figure 2: Growth of GA4GH resources over time¶

Figure 3: PubMed (Top 10 Journals)¶

Figure 4: Activity status of GA4GH GitHub repositories¶

Figure 5: Most recently updated GA4GH GitHub repositories¶

Figure 6: Interest metrics for GA4GH Github repositories¶

Figure 7: Functional categorization of GA4GH-related PyPi Packages¶

Figure 8: Most frequently released GA4GH-related PyPi packages¶

Figure 9: Searchable Table of GA4GH-related PyPi Packages¶

Total PyPI Packages: 82