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# 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.