A Snapshot version of the CGDS manual of operations from June 19th, 2020.

50f8e5a4 · Angelina Elizabeth Uno-Antonison · 50f8e5a4 · 50f8e5a4 · 50f8e5a4 · 50f8e5a4
Commit 50f8e5a4 authored Jun 19, 2020 by Angelina Elizabeth Uno-Antonison
--- a/.gitignore
+++ b/.gitignore
+.DS_store
+site/
+.idea
--- a/Dockerfile
+++ b/Dockerfile
+FROM python:3.7-alpine as development
+RUN pip install mkdocs==1.0.4
+
+EXPOSE 8000
+RUN mkdir /mkdocs
+VOLUME ["/mkdocs"]
+WORKDIR /mkdocs
+
+CMD ["mkdocs", "serve"]
+
+FROM python:3.7-alpine as build
+RUN pip install mkdocs==1.0.4
+
+EXPOSE 80
+COPY "." "/mkdocs"
+WORKDIR /mkdocs
+RUN mkdocs build
+
+FROM nginx:1.17-alpine as production
+
+COPY --from=build /mkdocs/site /usr/share/nginx/html
\ No newline at end of file
--- a/Jenkinsfile
+++ b/Jenkinsfile
+pipeline {
+  agent any
+  environment {
+    GITLAB_API_TOKEN = credentials('GitLabToken')
+    COMPOSE_PROJECT_NAME = "${env.JOB_NAME}-${env.BUILD_ID}"
+  }
+  stages {
+    stage('Static Analysis') {
+      agent {
+        docker { image 'gitlab.rc.uab.edu:4567/center-for-computational-genomics-and-data-science/utility-images/static-analysis:v0.6'}
+      }
+      steps {
+        wrap([$class: 'AnsiColorBuildWrapper', 'colorMapName': 'XTerm']) {
+          sh '/bin/linting.sh'
+        }
+      }
+      post {
+        success {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=success&name=jenkins_static_analysis\""
+        }
+        failure {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=failed&name=jenkins_static_analysis\""
+        }
+      }
+    }
+    stage('build') {
+      steps {
+        sh 'docker-compose -f docker-compose.production.yml build moo-production'
+      }
+      post {
+        success {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=success&name=jenkins_system_tests\""
+        }
+        failure {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=failed&name=jenkins_system_tests\""
+        }
+      }
+    }
+    stage('Publish Updates') {
+      when { branch 'master' }
+      steps {
+        // note -- using `weborg` until we have CGDS @TODO swap out
+        sh 'docker login gitlab.rc.uab.edu:4567 -u weborg -p ${GITLAB_API_TOKEN}'
+        sh 'docker-compose -f docker-compose.production.yml push'
+      }
+      post {
+        success {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=success&name=updates_published\""
+        }
+        failure {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=failed&name=updates_published\""
+        }
+      }
+    }
+    stage('swarm deploy') {
+      when { branch 'master' }
+      steps {
+        sh 'docker stack deploy --prune --with-registry-auth --compose-file docker-compose.production.yml moo-prod'
+      }
+      post {
+        success {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=success&name=swarm_deployed\""
+        }
+        failure {
+          sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=failed&name=swarm_deployed\""
+        }
+      }
+    }
+  }
+  post {
+    success {
+      sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=success&name=jenkins\""
+    }
+    failure {
+      sh "curl --request POST --header \"PRIVATE-TOKEN: ${GITLAB_API_TOKEN}\" \"https://gitlab.rc.uab.edu/api/v4/projects/1014/statuses/${GIT_COMMIT}?state=failed&name=jenkins\""
+    }
+  }
+}
\ No newline at end of file
--- a/README.md
+++ b/README.md
+# Center for Computational Genomics and Data Science Manual
+
+The Manual of Operations (MOO) for the Center of Computational Genomics and Data Science provides guidance to members
+of the center its mission and operations.  The manual of operations is a statically generated website using
+[MkDocs](https://www.mkdocs.org) which creates a static website from MarkDown files.  The following website
+<https://www.markdownguide.org/basic-syntax/> is a useful guide and cheatsheet to MarkDown syntax for formatting.
+
+## Local Development with Docker
+
+### Docal Pre-requesites
+
+* [Docker](https://www.docker.com)
+
+### Deploy Locally within Docker
+
+If you do not want to install Python or MkDocs directly onto your system, you can use docker and docker-compose to
+develop with locally. To start running the self-hosted mkdocs service to live update execute the following.
+> `docker-compose up`
+---
+
+## Local Development native on computer
+
+### Native Pre-requesites
+
+* [MkDocs](https://www.mkdocs.org/)
+
+### Installation
+
+#### MacOs  
+
+> [Homebrew](https://brew.sh/)  
+`brew install mkdocs`
+
+#### Windows
+
+> [Choclately](https://chocolatey.org/)  
+`choco install mkdocs`
+
+## Deploy Locally
+
+Use the following command to localy update and view hotloaded changes live.
+> `mkdocs serve`
+
+--
+
+## Add new pages
+
+There are two steps to add new pages to the manual of operations.
+>
+> 1. Create a new MarkDown file within the `docs/` directory.  MarkDown file names use Kebab Case naming scheme.
+An example is `helpful-uab-information.md`.
+> 2. Open the `mkdocs.yml` file within the root project directory.  Add a new line under the `nav` section within
+the YAML file with the following format `- <Page Name>: <mark-down-file-name.md>`.  The MkDocs shall order the menu
+the as the`nav` section in the `mkdocs.yml`.
+
+---
+
+## Production
+
+The following commands can only be executed if MkDocs is directly installed on the machine. However, this will rarely
+be needed when updating the MOO.
+
+### Build Website
+
+> `mkdocs build`
+
+### Build and Deploy to Gitlab Pages
+
+Reference the `.gitlab-ci.yml` file for configuration of Gitlab Pages continuous integration for deploying the mkdocs
+generated website to Gitlab pages.  
+> `mkdocs build -d public`
--- a/docker-compose.production.yml
+++ b/docker-compose.production.yml
+version: '3.4'
+services:
+  moo-production:
+    build:
+      context: .
+      target: production
+    image: gitlab.rc.uab.edu:4567/center-for-computational-genomics-and-data-science/manual-of-operations:v0.1
+    deploy:
+      labels:
+        - "traefik.enable=true"
+        - "traefik.docker.network=traefik-public"
+        - "traefik.docker.lbswarm=true"
+        - "traefik.http.routers.moo-production.rule=PathPrefix(`/manual-of-operations`)"
+        - "traefik.http.routers.moo-production.service=moo-production"
+        - "traefik.http.routers.moo-production.middlewares=moo-strip-prefix"
+        - "traefik.http.middlewares.moo-strip-prefix.stripprefix.prefixes=/manual-of-operations"
+        - "traefik.http.services.moo-production.loadbalancer.server.port=80"
+    networks:
+      - traefik
+
+networks:
+    traefik:
+        external:
+            name: traefik-public
\ No newline at end of file
--- a/docker-compose.yml
+++ b/docker-compose.yml
+version: '3.4'
+services:
+  moo-development:
+    build:
+      context: .
+      target: development
+    volumes:
+      - .:/mkdocs/
+    ports:
+      - "8000:8000"
+  moo-production:
+    build:
+      context: .
+      target: production
+    image: gitlab.rc.uab.edu:4567/center-for-computational-genomics-and-data-science/manual-of-operations:v0.1
+    ports:
+      - "80:80"
+    deploy:
+      labels:
+        - "traefik.backend=moo-production"
+        - "traefik.http.routers.moo-production.rule=PathPrefix(`/manual-of-operations`)"
+        - "traefik.http.middlewares.moo-strip-prefix.stripprefix.prefixes=/manual-of-operations"
+        - "traefik.http.routers.moo-production.middlewares=moo-production"
+        - "traefik.port=80"
+
+networks:
+  traefik-public:
+    external: true
--- a/docs/cgds-charter.md
+++ b/docs/cgds-charter.md
+# The Center for Computational Genomics and Data Science (CGDS)
+
+[TOC]
+
+## Team Purpose
+
+The Center for Computational Genomics and Data Science (CGDS) seeks to develop and apply tools and methods to uncover
+new and novel information that provide benefits for patients suffering from rare, undiagnosed, or misdiagnosed diseases,
+their families, and the people that care for them. CGDS focuses on interpreting molecular variation with regards to its
+correlation with patient phenotypes. We seek to identify and interpret causal molecular variation as well as variations
+that alter patients’ clinical severity and progression through modification of phenotype or through alteration of response
+to therapeutics (pharmacogenomics). Although we aim to generate knowledge that can be utilized for the study of human
+disease in general, we strive to produce and apply knowledge for individuals (patients, their families, and the clinicians
+who take care of them) in need of information to assist with clinical decision making in the present. CGDS diligently
+works to create and maintain a productive and friendly team environment where we continuously educate one another,
+contributeto scientific education, and disseminate new information locally and globally.
+
+The Center for Computational Genomics and Data Science (CGDS) seeks to advance delivery of precision medicine to
+patients and to advance research discoveries through the application multi-omics data science and innovations in alignment
+with the UAB School of Medicine (SOM) goals. Transfer of advancements is accomplished through education, patient care,
+basic research, translational research, and clinical research.
+
+## Duration and Time Commitment
+
+The CGDS work week consists of core hours that each member is expected to include in their workday; remaining hours in
+the work day are flexible.  We ask that you do your best to be in your office during core hours and schedule non-work
+appointments outside those core hours. Flexibility for team members is absolutely supported and does not reflect a lack
+of their commitment, but rather an acknowledgment of how life really happens.
+
+In return for this flexibility, team members are asked to be flexible in return, by working in the evenings or on
+weekends in exchange for taking time off during the week. Absences that can be planned outside of core hours (like
+doctor/dentist checkups) should be planned for early or late in the day. Minimizing absences within core hours whenever
+possible will help to dispel misunderstandings and reduce project impact.
+
+If you have an emergency or sickness, notify Liz and communicate with the team as soon as you can. Your commitment to
+communicating planned and unplanned events will reduce the possibility of tension and/or conflicts.
+
+## Scope
+
+At this point, the science in our areas of interest is just beginning to unravel the complexities of a multitude of
+questions. It’s important for us to keep focus on our goals and keep project scope in manageable tasks.
+
+We also acknowledge that every project we take on, contributes towards improving patient outcomes and patient’s quality
+of life even when negative results are achieved. This approach demands perseverance to stay on track, pursuing wherever
+the data may lead in planned increments.
+
+1. Development of expanded capabilities in the area of molecular diagnostics for oncology and rare disease and other
+mis- or undiagnosed diseases.
+2. Organization of data science innovations across the UAB SOM as a whole.
+3. Driving or enabling differentiation and growth for key UAB clinical service lines using omics-based data science.
+4. Supporting the empowerment of physicians by providing the information they need to enable data science driven
+precision care.
+5. Development of grant revenue streams for Data Science related to; precision medicine, phenotype-to-genotype studies,
+polygenic risk score analyses, pharmacogenomics, molecular diagnostics, etc.
+6. Development of materials for education of students, residents, and healthcare providers.
+7. Evaluation, prioritization, and development of partnership and other opportunities both within and external to UAB.
+8. Development of philanthropic opportunities in the area of -omics data science in support of UAB SOM missions.
+
+## Keys to Success
+
+Team success is achieved by building on existing talent, relationships, investments, and accomplishments. Success also
+relies on strengthening intra- and inter- institution communications and collaborations. It is important to initiate,
+support, and reinforce interdisciplinary collaborations among our CGDS teams and with UAB researchers, clinicians,
+pathologists, laboratory administrators, and other specialists and other teams who bring important knowledge to these
+efforts. Although there may be a gap between research goals and the application of new discoveries in clinically-useful
+manner, our team will work towards development of tests and procedures that useful for patients and can be reimbursed
+through health insurance providers.
+
+## Members (Nov 2019)
+
+In order to meet the needs of our distinctive units, the Department of Pathology, the Department of Pediatrics, the UAB
+School of Medicine Omics-based Data Science Program, and the clinical- and research-focused Worthey Lab Research Program,
+teams of software developers, data scientists, statisticians and researchers peopled by junior and senior research
+scientists, and students will focus their efforts into Software Development, Data Science, and Molecular Variation
+Interpretation.  Many CGDS members will work across many of these foci including an administrative associate, the lab
+manager, a system administrator, and research IT. This structure allows CGDS to define teams and reporting structures,
+and ensures cohesion among the teams given that success will require significant amounts of cross team interaction.
+
+### Dr. Liz Worthey
+
+**Director** for the _Center for Computational Genomics and Data Science_ within the departments of _Pediatrics and
+Pathology_ in _UAB School of Medicine_  
+**Director** of the _Bioinformatics Section in Division of Genomics Diagnostics and Bioinformatics_ within the
+department of _Pathology_ in _UAB School of Medicine_  
+**Associate Director** in _Hugh Kaul Precision Medicine Institute_  
+**Associate Professor** _Pediatrics and Pathology_  
+**Scientist** the _O’Neal Comprehensive Cancer Center_  
+
+### Arthur Weborg
+
+Software Architect - Genomics
+
+### Angelina Uno-Antonison  
+
+Software Developer III - Genomics
+
+### Donna Brown  
+
+Molecular Variant Analyst
+
+### Brandon Wilk  
+
+Software Developer III - Genomics
+
+### Dr. Manavalan Gajapathy
+
+Data Scientist - Genomics
+
+### Alex Moss
+
+Software Developer I - Genomics
+
+## Team Sponsor Dr. Selwyn Vickers
+
+Senior Vice President of Medicine
+Dean of the University of Alabama at Birmingham School of Medicine
+
+Dr. Vickers has held these posts since October 2013. He is a world-renowned surgeon, pancreatic cancer researcher, and
+pioneer in health disparities research. Dr. Vickers is a member of the National Academy of Medicine
+(Institute of Medicine) and of the Johns Hopkins Society of Scholars. Dr. Vickers personally recruited this team to UAB.
+
+## Other sponsors or key stakeholders
+
+* **Dr. Matt Might**
+* **Dr. George Netto**
+* **Dr. Bruce Korf**
+* **Dr. Mitch Cohen**
+
+## Desired End Result
+
+We will focus on development and application of tools and methods to identify and interpret causal molecular variation
+i.e. ending of diagnostic odysseys, as well as identification of variation that otherwise alters a patient's clinical
+picture through modification of their phenotype or through alteration of response to therapeutics (pharmacogenomics).
+Critically our goals are clinical; although we aim to generate generalizable knowledge for future studies, we strive to
+produce and apply knowledge for these individuals today; not ten years down the road in their journey.
+
+## Supporting Resources
+
+* [UAB School of Medicine Pediatrics Department](https://www.uab.edu/medicine/peds/)
+* [UAB School of Medicine Pathology Department](https://www.uab.edu/medicine/pathology/)
+* Pediatrics IT
+* [Children's of Alabama](https://www.childrensal.org/)
+* [UAB IT Research Computing Department](https://www.uab.edu/it/home/research-computing)
+* [Hugh Kaul Precision Medicine Institute](https://www.uab.edu/medicine/pmi/)
+* [O'Neal Comprehensive Cancer Center](https://www.uab.edu/onealcancercenter/)
+
+The supporting resources include other people not assigned as team members but who aid our overall purpose.  Other
+resources may be called upon to supply needed resources (blue prints, meeting rooms, travel budgets, corporate
+authority, software, etc.)
+
+## Management of Projects
+
+Due to the vast variety of project types within the CGDS, each project shall have a project charter using the CGDS
+project charter template.  The Project Charter will be shared among all project members to communicate scope and work
+required. In regards to reports, the charter informs report format, method of delivery, frequency of delivery, and to
+whom it must be delivered to.
+
+## Deliverable
+
+Project charters characterize the summation of work within the CGDS.  This document defines the project intentions,
+resources, activities, and goals.  Each project charter uses the CGDS project charter template as a guide to ensure all
+members understand the scope and purpose of the work.  Goals within the project charter must map directly to the goals
+of the CGDS which correspond directly from the UAB School of Medicine.  The individual goals for members of the CGDS
+must fall within the scope of the project’s goals. Project charters also define project status reports and final
+project deliverables.
--- a/docs/cheaha-cluster.md
+++ b/docs/cheaha-cluster.md
+# UAB Compute Cluster a.k.a. Cheaha
+
+[TOC]
+
+## Overview
+
+Cheaha is a large, multi-unit computational system for running massively
+parallel compute tasks. It is managed by the [UAB Research Computing Group](https://www.uab.edu/it/home/research-computing)
+
+Cheaha is currently the fastest supercomputer in the state of Alabama with a theoretical throughput of
+approximately 450 TFlop/s (HUGE COMPUTE!) and consists of over 3000 CPU cores and 72 NVIDIA-P100 GPU's. Cheaha is
+supported by a high-speed parallel filesystem (GPFS) that can store 6 PB non-redundantly and 4 PB redundantly (with
+more to come!) interconnected by a high speed infiniband network. UAB researchers use Cheaha for wide variety of
+research such as genomics, neuro-imaging, machine learning, statistical genetics, cancer detection etc.
+
+Use of this resource is governed by the
+[UAB Acceptable Use Policy for Computer and Network Resources](https://www.uab.edu/policies/content/Pages/UAB-IT-POL-0000004.aspx)
+
+For more information on Cheaha and the tools available to support research please review the documentation:
+<http://docs.uabgrid.uab.edu/wiki/Cheaha>
+
+## Access
+
+To get setup with cluster access you'll need your BlazerID and send an email to the cluster
+support group (`support@listserv.uab.edu`).
+
+You can use this template email filled in with your information to make this request.
+
+```text
+Hello!
+
+My name is __YOUR_NAME__ and I’m a __TITLE__ in Dr. Liz Worthey’s lab.
+I’d like to request access to the cluster for our Genomics, Genetics and Data
+Science research. In particular I will be doing data analysis, pipeline
+development, and genomics research using the compute resources of the cluster.
+
+Sincerely,
+
+YOUR NAME
+TITLE
+Dr. Liz Worthey’s Lab
+Center For Computational Genomics and Data Science
+```
+
+## Storage spaces
+
+* Scratch Space
+  * 1 TB of fast storage (i.e. close to the compute for super fast input/output)
+* Home Space
+  * 50 GB of fast-ish storage for small data, scripts, small analyses, etc.
+* User Data Directory
+  * 20 TB of fast-ish storage for larger data needs
+* Lab/Project Space
+  * 50 - 100 TB per lab of fast-ish storage for project level data and analysis
+* Commodity Storage (coming soon!)
+  * ??? TB of slower storage but HUGE for bigger datasets
+
+## Submitting Jobs
+
+You can SSH into the cluster via
+
+```bash
+ssh BLAZERID@cheaha.rc.uab.edu
+```
+
+The cluster uses the Slurm queue management system (stands for Simple Linux Utility for Resource Management) for
+scheduling, distributing, and managing compute "jobs". A "job" is just a general term used to describe doing a specific
+task, or set of tasks (specified in script) on the compute contained within the cluster.
+
+For a complete description and tutorial of writing and executing jobs on the cluster see Research Computing's helpful
+[guide](https://docs.uabgrid.uab.edu/wiki/Slurm) on Slurm and executing compute tasks on the cluster. You can also check
+out the below tutorial for a quick high level view of the cluster.  
+
+## Python on the Cluster  
+
+Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, that
+aims to simplify package management and deployment. Package versions are managed by the package management system conda.
+CDGS plans on using conda on the cluster for multiple projects involving the use of python.
+
+### Conda Shortcuts for cluster
+
+* Enabling Conda Module on Cluster  
+  `module avail Anaconda`
+
+* Creating new Conda Environment  
+  `conda create --name test_env`  
+  Packages can be included within the new environment with a similar command  
+  `conda create --name test_env PACKAGE_NAME`
+* List available virtual environments available  
+  `conda env list`  
+  Virtual environment with the asterisk(\*) next to it is the one that's currently active
+* Activating conda virtual environment  
+  `source activate test_env`
+* Deactivating Virtual Environment  
+  `source deactivate`
+* Export Conda virtual environmnet to share  
+  `conda env export -n test_env > environment.yml`
+* Creating Conda Virtual Environment from environment.yml  
+  `conda env create -f environment.yml -n test_env`
+* Deleting a Conda Virtual Environment  
+  `conda remove --name test_env --all`
+
+For a complete tutorial and for a most up-to-date version, please use the tutorial from
+[UAB Research Compute's Anaconda Wiki](https://docs.uabgrid.uab.edu/wiki/Anaconda).
+
+## Briefings and Highlights
+
+![slide01](img/cheaha_101/Slide01.png)
+![slide02](img/cheaha_101/Slide02.png)
+![slide03](img/cheaha_101/Slide03.png)
+![slide04](img/cheaha_101/Slide04.png)
+![slide05](img/cheaha_101/Slide05.png)
+![slide06](img/cheaha_101/Slide06.png)
+![slide07](img/cheaha_101/Slide07.png)
+![slide08](img/cheaha_101/Slide08.png)
+![slide09](img/cheaha_101/Slide09.png)
+![slide10](img/cheaha_101/Slide10.png)
+![slide11](img/cheaha_101/Slide11.png)
+![slide12](img/cheaha_101/Slide12.png)
+![slide13](img/cheaha_101/Slide13.png)
+![slide15](img/cheaha_101/Slide15.png)
+![slide16](img/cheaha_101/Slide16.png)
+![slide17](img/cheaha_101/Slide17.png)
--- a/docs/continuing-education.md
+++ b/docs/continuing-education.md
+# Continuing Education
+
+[TOC]
+
+All of us are expected to be engaged in continuing to build our expertise in pursuit of achieving our goal to advance
+science. As a member of this group you are required to document your efforts by **accumulating at least 12 continuing
+education (CE) hours per year**, with **at least one hour in every quarter**.
+
+## CE Activities
+
+Any of the following activities can satisfy that goal.
+
+* Attend seminars related to project goals
+* Attend individual sessions at meetings/conferences (document each session/talk separately)
+* Participate in workshops
+* Attend Grand Rounds in Birmingham or Huntsville
+* Complete an online course connected to your work
+* Working on higher education training relevant to the field or position held (i.e. a Masters, Ph. D., etc.)
+
+## CE Logging
+
+Create and maintain a log of your activities towards this goal for each calendar year. A template is set up in
+[Box/CGDS/General/Continuing Education](https://uab.box.com/s/pbjryninz93xkw38xbaq1qdt4a4sh912). Open the template then
+Save As and add your name to the file name within the /Continuing_Education folder. Add new CE activities to this same
+file throughout your tenure with CGDS.
+
+For each activity record:
+
+* Title
+* Activity type
+* Location (URL if online course, course(s) code when applicable)
+* Date(s)
+* Time spent:  
+  Brief statement describing the activity and it furthered your knowledge
+
+For example:
+
+```md
+Grand Rounds @ Hsv 24-Sep-19 45min
+
+M+M presentation by 3rd yr resident on patient w/Pyridoxine-dependent epilepsy and the
+problems encountered getting patient treatment established due to mistakes and unnecessary
+delays. Note: Perhaps EHR could support rare disease alerts for professionals. Also resident
+was unaware of how to test for this condition so some education in OMIM, and other databases
+to support diagnosis would be useful.
+```
+
+If you have other activities you would like to add to this list to fulfill the requirements, please check with Liz to
+get approval. Also note that HIPAA training does not count toward this requirement.
--- a/docs/data-policies.md
+++ b/docs/data-policies.md
+# Data Policies and Standards
+
+[TOC]
+
+## Locations
+
+The following table describes what types of data/files should go where for CGDS
+
+| Data Type | Examples | Storage |Location |
+| Anything containing PHI                         | Pictures, Medical Records, Clinical Descriptions  | Box     |
+<https://uab.app.box.com/>                                                                |
+| Project analysis files not used for computation | IRB Documents, project charter, deidentified data | Box     |
+CGDS/Projects/{project identifier}/                                                   |
+| Project sequence files                          | Fastqs                                            | Cluster |
+/data/project/worthey_lab/projects/{project identifier}/raw/{sample identifier}/      |
+| Project analysis files used for computation     | BAM, VCF, output from other tools                 | Cluster |
+/data/project/worthey_lab/projects/{project identifier}/analysis/{sample identifier}/ |
+
+## Box
+
+In general here's what the overall layout should be of the Box directories:
+
+```text
+.
+├── Alexander and Worthey Labs Collaboration
+└── CGDS
+    ├── General
+    │   ├── Grants\ Info
+        ├── Job\ Descriptions
+    │   ├── LabCharter
+    │   └── MeetingNotes
+    └── Projects
+        ├── CF\ Projects
+        │   ├── CF-Brothers\ Three
+        │   ├── CF-First
+        │   └── Gerber\ CF
+        ├── Data\ Requests
+        ├── KidsNetwork\ RO3
+        ├── MECFS
+        └── TSC
+```
+
+### Collaborations
+
+From time to time, it is important for our lab to share files with other labs. To this end, we will create collaborative
+directories in Box that grant access between our lab and the collaborators lab. For example, a collaboration directory
+for work done with the Alexander lab would exist at the same level as the Root CGDS directory (see below). When first
+entering Box you would see the directory `Alexander and Worthey Labs Collaboration` at the same level as the `CGDS`
+directory (see above diagram of the directory structure).
+Remember the collaboration directory is for sharing large-ish files and results between the labs. Permissions are set
+according to the particular collaboration needs.
+
+### Root CGDS Directory
+
+The root directory in Box is for all files related to the CGDS. The only directories within the root directory are the
+`Projects` and `General` directories. Descriptions and organization of those directories are below.
+
+### Projects Directory
+
+This directory is the space for storing all "project" related data. The term `Project` is meant to encompass a wide
+range of activities executed in the lab. A project is not defined by the amount of time, size, space, or work it will
+involve. A project is used to describe and organize information about a topic of work, research, or development. For
+example the following all define projects in the lab (this is not an exhaustive list):
+
+- application development
+- pipeline development
+- grant funded research