ABI Knowledge Base

Table of Contents

Research Projects

This section documents ongoing and past research projects at ABI. Each project has its own page with details about goals, team members, data locations, and analysis methods.

Active Projects

Project Description Lead Status
cfDNA Cell-free DNA analysis *TODO* Active
Microbiome *TODO: brief description* *TODO* Active
Vine *TODO: brief description* *TODO* Active
*TODO* *Add more projects as needed* *TODO* *TODO*

Completed Projects

*TODO: Move completed projects here with a summary of outcomes.*

Project Description Completed Outcome
*TODO* *TODO* *TODO* *TODO*

Project Data Locations

Each project has a shared data directory at: 

/mnt/nas1/proj/<project_name>/
Project Data Path
cfDNA /mnt/nas1/proj/cfdna/ *TODO: confirm*
Microbiome *TODO*
Vine *TODO*

Creating a New Project Page

When starting a new project at ABI, please create a wiki page to document it. Use the template below.

How to create the page

  1. Go to https://wiki.abi.am/projects:<project_name> (e.g., projects:my_new_project).
  2. Click “Create this page”.
  3. Copy the template below and fill it in.
  4. Save the page.
  5. Add a link to your project in the table above on this page.

Project Page Template

Copy this template when creating a new project page: 

====== Project Name ======

===== Overview =====

Brief description of the project goals and scientific questions.

===== Team =====

^ Name ^ Role ^ Contact ^
| *Name* | *PI / Lead / Analyst* | *email* |

===== Data =====

^ Dataset ^ Location ^ Description ^ Size ^
| Raw data | /mnt/nas1/proj/project/raw/ | FASTQ files from sequencing | *X* GB |
| Results | /mnt/nas1/proj/project/results/ | Analysis outputs | *X* GB |

===== Methods =====

Brief description of the analysis workflow. Link to relevant [[pipelines:start|pipelines]] and [[scripts:start|scripts]].

  - QC: [[scripts:qc|FastQC + MultiQC]]
  - Trimming: [[scripts:adapter_and_quality_trimming|fastp]]
  - Alignment: [[scripts:alignment|BWA mem]]
  - Variant calling: *TODO*

===== Results =====

Summary of key findings, links to reports, or references to publications.

===== References =====

  * Relevant papers, grant information, or external resources.

===== Notes =====

Any additional information, caveats, or TODOs for the project.

See Also