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projects:start [2025/03/10 09:53] – created avprojects:start [2026/04/08 00:27] (current) – updated projects page av
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-Here are (some of) the existing projects at ABI:+====== Research Projects ======
  
-  * [[projects:cfdna|cfdna]] +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. 
-  * [[projects:microbiome|microbiome]] + 
-  * [[projects:vine|vine]]+===== 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
  
-Feel free to add your own projects as well.