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# Projects
[TOC]
## Overview
Any, and all, projects initiated by CGDS, or in collaboration with other entities, need to follow this set of steps.
1. Incubation Period
2. Review to `Move Forward` or `Retire`
3. Chartering
4. Chartering Peer Review
5. Active and Maintenance
1. Analysis/Research
2. Software Development
Below each step is reviewed in detail.
## Incubation Period
This is the informal brainstorming type sessions about a topic. It is fairly free form, as needed, for the
conceptualization of a project. For instance it could be a simple chat between colleagues or an idea from Liz or a cool
paper. This process is less structured and still under construction/definition.
Things to define in this step:
* Outside collaborators/integrations (if applicable)
* Who's gonna pay (e.g. grant, foundation, lab funds, etc.)
* Need/justification (liz said so is good enough, sometimes ;) )
* Basic scope
## Review and Move Forward or Retire
Following the incubation period, a decision needs to be made if the project is a go/no-go with Liz and relevant parties.
This is done during the weekly group meeting or another meeting. If the project is a go it can proceed to a `Kick Off`
otherwise, it can be retired with a note in Box.
## Chartering
The chartering stage is the initial formal organization of the project. This phase involves filling out the
`Chartering worksheet` in Box. The Project Charter is ready to be created in Wrike when the worksheet is complete.
Visit the [Project Charter](project-charter.md) on how to create the Project Charter in Wrike.
## Chartering Peer Review
Once `Project Chartering` is complete, several colleagues peer review the charter in Wrike. Organization
is key to projects being tracked and statused for success. Once the peer reviewers are satisfied with the charter
and project setup in Wrike the project is ready for work.
## Active and Maintenance
At this point, the project is active and/or maintained (either to completion, continued development, maintenance,
and retirement). Depending on the nature of the project (i.e. an analysis/research project or software development
project) this is a branching point where one of two sub-paths is taken. In the case of
[Analysis/Research](#analysisresearch) the project has certain reporting and tracking associated that wouldn't otherwise
be necessary for software. In this case, custom fields are filled out in Wrike as more details become available for the
given project. For software development projects they will follow the [Software Development](#software-development)
sub-path, with it's own organization and requirements. Some of these will be similar to those in the Analysis/Research
sub-path.
### Software Development
The software development process in CGDS is under constant refinement Read [Software Development Getting Started Page](dev-getting-started.md)
for guidelines and best practices. Continue reading through all of the sections listed under `Code Development`.
### Analysis/Research
Specifics to guide you through an Analysis/Research project is documented in a series of Standard Operating Procedures
(SOPs). Briefly the steps are:
⦁ Initiating and tracking your project’s progress from beginning to completion
⦁ Obtaining NGS sequencing services and other data
⦁ Analysis and reporting of those data
⦁ Support and communication with project collaborators
* [A001 - Beginning an analysis project](https://uab.box.com/s/u2ojq55f83u5l5yqh6tsday6jmzje2xd)
Initiating and tracking your project’s progress from beginning to completion
* Obtaining NGS sequencing services and other data: [List of SOPS](https://uab.box.com/s/p1m7tu8i7a893vp1nx876gipreoybvve)
* [A010 - Analysis of WGS or WES using tertiary software](https://uab.box.com/s/737qssvpcsrwf42s5u797usvvgpiawss)
Analysis and reporting of those data
* Support and communication with project collaborators