====== 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 ^
| [[projects:cfdna|cfDNA]] | Cell-free DNA analysis | *TODO* | Active |
| [[projects:microbiome|Microbiome]] | *TODO: brief description* | *TODO* | Active |
| [[projects:vine|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:

<code>
/mnt/nas1/proj/<project_name>/
</code>

^ 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 ===

  - Go to ''%%https://wiki.abi.am/projects:<project_name>%%'' (e.g., ''projects:my_new_project'').
  - Click "Create this page".
  - Copy the template below and fill it in.
  - Save the page.
  - 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:

<code>
====== 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.
</code>

----

===== See Also =====

  * [[pipelines:start|Pipelines]] -- Bioinformatics workflows
  * [[databases:start|Databases & Reference Data]] -- Shared reference data
  * [[scripts:start|Scripts]] -- Reusable analysis scripts