Code & Software

As part of the Aligning Science Across Parkinson’s (ASAP) initiative’s commitment to open science, we believe it is critical that ASAP-funded work can be leveraged by the research community. Supporting the development of open resources, and sharing outputs such as code and software, benefits the scientific community by enabling researchers to build upon existing work.

Our Approach to Code Sharing

We require grantees to share code in a publicly accessible repository with a permanent identifier. This includes scripts, software, packages, macros, pipelines, and any other code used for data manipulation. An assessment of code sharing in ASAP-funded publications showed that the policy’s implementation led to an increase in code sharing at publication.

Read Our Blog Post

GP2 GitHub

GP2 has its own repository on GitHub, GP2Code, which follows best practices and industry standards in open science code sharing. Visit GP2Code to explore examples of published and ongoing GP2 projects developed within GitHub’s community-based framework.

Learn More

CRN Software Highlights

Several Collaborative Research Network (CRN) Teams have utilized their skills to produce software packages for analysis and modeling. Below we highlight a few examples.

SynBot

SynBot is an open-source, Image J-based software developed by CRN Team Calakos that automates analysis of synapses from immunofluorescence images.

Use SynBot

TEtoolkit

TEtoolkit is a suite of software packages developed by CRN Team Jakobsson to enable analysis and quantification of transposable elements in RNA sequencing data.

Use TEtoolkit

PyRates

PyRates is a Python-based software package developed by CRN Team Cragg for modeling neural networks and other complex, dynamic biological systems. Its extensions, PyCoBi and RectiPy, expand its modeling capabilities.

Use PyRates

Code in the ASAP Catalog

Our initiative is accelerating the pace of discovery for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. Browse our Catalog to view all ASAP-supported code & software.

Browse Our Catalog