Vanderbilt University offers an ideal setting for its new Department of Biostatistics established in September 2003. The department offers a full array of biostatistical support with an emphasis on establishing long-term collaborative relationships with investigators in accomplishing the research mission of the institution. The Department currently has 33 faculty biostatisticians and 27 staff Masters-level biostatisticians, 7 computer systems analysts, and 10 administrative staff members. The department has one division, the Division of Cancer Biostatistics. See more about the division...
The department occupies approximately 8148 square feet in Medical Center North including two conference rooms.
The department operates a collaborative web site; the entire site is a wiki. We encourage department members to use the site as a repository for meeting notes, grant development, tutorials and the like. The wiki allows for rapid hosting of new content and fosters collaborative work, hosting of teaching materials, and managing clinics. We view the site as a constantly growing knowledge base that has very many contributors.
The IT Team supports various hardware and software platforms, departmental networking, computer performance issues, software acquisition and installation, and task specific programming. The team has programming experience with a wide array of programming languages and techniques to support programming design, database design, statistical programming, web applications, and high performance computing. The team has extensive experience collecting data from disparate sources and assembling the data into clean, analysis-ready data sets.
Members of the group have experience with R Programming, building R packages, supporting package repositories, and making submissions to CRAN. Biostatistics programmers maintain the Hmisc and rms packages. The rApache, Rook, brew, RMySQL, canvas, datamap, gearman, redcap, rmemcache, and MingSWF packages are developed and/or maintained here. Work is being done with RStudio to make it possible to easily create interactive web interfaces from R, to improve HTML rendering of tables in R, and to facilitate the deployment of R web applications. The popular PS: Power and Sample Size Calculation program was developed and is maintained by a member of the IT Team.The Biostatistics IT Team understands the issues surrounding confidentiality and is committed to compliance with data privacy rules and regulations.
The IT Team members are Cole Beck, Thomas Dupont, Shawn Garbett, Zhouwen Liu, Dale Plummer, and Jeremy Stephens.Skill Set | IT Team Members |
---|---|
Statistical analysis (under the direction of statisticians) | All |
R Programming, building R packages, supporting package repositories, and submissions to CRAN | ColeBeck, CharlesDupont, ZhouwenLiu, JeremyStephens, Shawn Garbett |
Contributions to the RStudio product | JeffreyHorner |
SAS Programming | DalePlummer, ZhouwenLiu |
Stata Programming, including contributions to the base Stata product | DalePlummer |
Web applications using R and RApache, Shiny, Ruby and Rails, PHP, and other web application toolsets | All |
Web libraries: Sinatra, .NET, Maria (Javascript MVC framework); Qt (desktop GUI library) | JeremyStephens |
Acquisition and preparation of data for the production of analysis data sets ("data cleaning") | All |
Programming in C, C++, Ruby, Perl, PHP, Python, Java, Javascript, HTML, CSS, Go | ColeBeck, CharlesDupont, ZhouwenLiu, JeremyStephens, Shawn Garbett |
Design and implementation of databases using MySQL, SQL Server, PostgreSQL, and other SQL-based database packages | All |
Design, implementation, and support of REDCap databases | All |
Support of Linux based servers (installation, maintenance, scripting, backup, performance management) | ColeBeck, CharlesDupont, DalePlummer, JeremyStephens, Shawn Garbett |
Support of desktop computers (Linux, Macintosh, Windows; installation, maintenance, backup, help) | ColeBeck, DalePlummer |
Hardware work: selection, troubleshooting and repair, peripherals, networking, printers, etc. | ColeBeck, DalePlummer |
Production of desktop applications using various languages | All |
Management of clinical trials data | All |
Understanding and compliance with data privacy rules and regulations | All |
High performance computing and use of Vanderbilt's ACCRE cluster | ZhouwenLiu |
LaTeX, knitr, Sweave | ColeBeck, CharlesDupont |
There are also a number of desktop computers running the Windows operating system. These computers participate in the Vanderbilt active directory domain.
All computers that are connected to the Vanderbilt network are protected from insecure outside access by the Vanderbilt perimeter firewall. Access to internal computers from external locations require the use of Vanderbilts VPN system or the SSH network protocol for secure data communication.
All computers and printers are connected to the Vanderbilt campus network that provides high speed access to e-mail and the Internet.
Printing services are provided by 3 Xerox Phaser 6360DN color laser printers.
VUMC provides a secure file transfer web application produced by Accellion that gives the ability to send large files securely. The department also provides DataHippo, a web application for secure transfer of data containing confidential information.The department also has fax, scanner, and copy machines and other standard office equipment. There is a secure document disposal system in our office suite.
Department of Biostatistics staff and faculty project effort is billed directly to each project as a percentage of salary and fringe benefit expenses. In addition, a scientific resource fee, pro-rated per FTE effort allocated to the project, is billed to each project for allowable expenses necessary to perform the work of biostatisticians and computer systems analysts. These expenses are directly related to ensuring that each biostatistician has access to appropriate tools and other scientific resources that support each project, including the array of technologies needed to manage and analyze many types of data across the spectrum of biomedical research.
The biostatistics scientific resource fee is administratively managed through the Biostatistics Collaboration Center, a VUMC sponsored core resource. The VUMC Office of Research (OOR) annually reviews the BCC to ensure best compliance with all applicable federal and state regulations, including uniform administrative requirements, cost principles, and audit requirements for federal awards. Rates are adjusted annually to ensure that the BCC operates on a strict non-profit cost recovery basis. The scientific resource fee is billed on a monthly basis via the OOR centralized core billing system Core Ordering and Reporting Enterprise System (CORES).In 2010 the Department of Biostatistics began allocating M.S. staff biostatistician time to projects using hourly billing based on a core-standard 1,500 billable hour work year. A change is being made to enhance the culture of collaboration and academically productive partnerships.
Beginning July 1, 2014 all biostatistics staff and faculty effort is being billed directly to each project as a percentage of salary and fringe benefit expenses. In addition, a scientific resource fee is being billed to each project for allowable costs related to providing cutting-edge biostatistics support. Changes have been made to the model and some costs have been reduced related to providing this service. Therefore, your overall costs will be reduced with the new rate. The department utilizes robust computing technologies and innovative methodologies to manage complex analyses. This scientific resource fee covers costs necessary to perform the work of biostatisticians and computer systems analysts. These resources are directly related to the many technologies used and types of data generated across multiple disciplines that biostatisticians must competently handle. The scientific resource fee will be billed on a monthly basis via the Core Ordering and Reporting Enterprise System (CORES).
The growth in the number of biostatisticians in the Department of Biostatistics comes solely from the growth of funded biomedical research requiring statistical design and analysis. The Department of Biostatistics faces real personnel support costs in meeting the demands from other departments and centers, and the School of Medicine has created a model described here that allows the costs to be recovered from the sources requesting the assistance.
These changes have been reviewed and approved by executive leadership of the School of Medicine.
Career development and methodologic mentoring is provided for all faculty. There is a meeting each month for all tenure-track faculty and another meeting for non-tenure-track faculty. Monthly faculty meetings are used to discuss ways to improve our research infrastructure and collaborations with biomedical researchers. These meetings are also used to seek opportunities for between-faculty methodologic collaboration.
The department has a weekly seminar, daily biostatistics clinics, and weekly clinics for the R statistical computing language. Frequently, collaborators and former mentors are brought in to make presentations in the seminar series. The daily clinics, which are intended primarily for biomedical researchers and are staffed by an average of five biostatisticians per day, have also provided a significant amount of methodologic assistance for biostatisticians, in two ways: by allowing them to witness how other, often more senior, biostatisticians solve problems in biomedical research, and by providing time for biostatisticians to ask each other questions. In addition to these opportunities, the faculty have an informal luncheon two days per week to discuss statistical philosophy and theory and career development.
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2525OfficeAssignments.png | manage | 43 K | 11 Nov 2013 - 11:21 | DalePlummer |