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---+ Department of Biostatistics at Vanderbilt University School of Medicine

---++ Facilities and Resources

A related topic is [[Main.GettingStartedBiostatistics][Getting Started at Vanderbilt Biostatistics]].

---+++ Facilities

The Department of Biostatistics at Vanderbilt University Medical Center was established in 2003 by Dr. Frank Harrell. Dr. Yu Shyr was recruited as the new chair effective September 1, 2017. The department offers a full array of biostatistics, bioinformatics, and data management support, with an emphasis on long-term collaborative relationships with investigators in accomplishing the research mission of the institution. The department currently has 43 primary and 8 secondary faculty in biostatistics. They are supported by 37 staff data scientists (MS and PhD level), 14 computer systems analysts/IT staff, and 6 administrative staff members. The department houses the Center for Quantitative Sciences. Central to the department’s mission is national leadership in methods and measurement development. 
The department operates the Data Science Shared Resource for the Vanderbilt Ingram Cancer Center, the Statistics and Methodology Core for the Vanderbilt Kennedy Center for Research on Human Development, and the Biostatistics Collaboration Center (BCC), a recharge center. Additionally, the department operates the Biostatistics Shared Resource for the Vanderbilt Institute for Clinical and Translational Research (VICTR) Methods program (i.e. CTSA). The department also partners with clinical departments on formal collaboration plans. These plans create a formalized relationship between biostatisticians and investigators, funded by the clinical department, to nurture an environment where investigators and biostatisticians together are developing new programs of research that are rigorous in design from inception. 

The department operates the Data Science Shared Resource for the Vanderbilt Ingram Cancer Center, the Statistics and Methodology Core for the Vanderbilt Kennedy Center for Research on Human Development, and the Biostatistics Collaboration Center (BCC), a recharge center. Additionally, the department operates the Biostatistics Shared Resource for the Vanderbilt Institute for Clinical and Translational Research (VICTR) Methods program (i.e. CTSA). The department also partners with clinical departments on formal collaboration plans. These plans create a formalized relationship between biostatisticians and investigators, funded by the clinical department, to nurture an environment where investigators and biostatisticians together are developing new programs of research that are rigorous in design from inception. 

The strong link between the Department of Biostatistics and VICTR (Vanderbilt’s institutional research infrastructure, Gordon Bernard, MD, Executive VP for Research and CTSA PI) ensures access to additional resources should they become necessary. For example, VICTR supports the Vanderbilt Coordinating Center, a comprehensive clinical trial coordinating group, which can provide additional expertise and personnel in trial conduct should it be needed. VICTR also coordinates activities such as the Institutional Review Board, the REDCap program, integration of clinical research billing plans into the medical record, and investigator training programs. 

The department also holds a walk-in Biostatistics [[Clinics][Clinic]] each day of the week from noon to 1:15pm. These clinics are for the entire Vanderbilt and Meharry Medical College community to provide assistance in study design, measurement refinement, statistical analysis, and statistical interpretation of their results and of journal articles. Clinic staff also assist investigators in navigating all the quantitative resources at Vanderbilt.

The department occupies approximately 12,624 square feet on the eleventh floor of the 2525 West End Avenue building, including two conference rooms, and an additional conference room centrally located in Medical Center North.

The conference rooms are equipped with projectors and screens.  Ubuntu Linux based computers are placed in each room and may be used for presentations and live analyses.  Presenter's laptops may be connected to the projectors.

---+++ Department Wiki

The department operates a [[http://biostat.mc.vanderbilt.edu][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.

---+++ IT Team

%INCLUDE{"Main.ITTeamSkills"}%

---+++ Desktop Computers

Each faculty and staff member is provided with a well equipped desktop computer and a wide range of software.

Individual workstations are systems produced by [[http://www.system76.com/][System76, Inc.]], Dell, or Apple. Typically, these systems have Intel Core i7 processors or better, 16 GB of memory or more, and at least 500 GB of disk space.  The R package for statistical computing and graphics is installed on all analysts' workstations. The department supports approximately 50 desktop workstations.

All computers that are connected to the VUMC network are protected from insecure outside access by the VUMC perimeter firewall. Access to internal computers from external locations require the use of VUMC VPN system or the SSH network protocol for secure data communication.

There are also a number of desktop computers running the Windows operating system. These computers participate in the Vanderbilt active directory domain.

Files on the desktop computers are backed up on a regular basis using a service provided by [[http://www.accre.vanderbilt.edu/][Advanced Computing Center for Research and Education (ACCRE)]]. ACCRE uses the [[http://www.teradactyl.com/products/teradactyl-software/][TiBS]] enterprise backup system that is produced by [[http://www.teradactyl.com/][Teradactyl, LLC]].  This backup scheme is designed to allow for recovery after device has failed or if a file has been accidentally deleted. It is important to note that this is not an archival backup service.  We cannot restore a file from any time in the past.  The ACCRE tape service should be able to restore from 3 to 6 months in the past, depending on the volume of data being backed up.  But if you delete a file and then 3 years later want it restored, you are out of luck.

All computers are connected to the Vanderbilt campus network that provides high speed access to e-mail and the Internet.

---+++ Servers

The department operates a number of server computers:
   1 a custom built system with two 64-bit Intel processors, 96 GB main memory, 1 TB of mirrored disk storage. This system acts as a compute server. Its primary purpose is to run jobs written in the R programming language that need fast processors and/or large amounts of memory. The server's operating system is 64-bit Ubuntu Linux. (statcomp2.app.vumc.io). See [[Main.StatCompServerInfo][(statcomp2.app.vumc.io Information]] for more information.
   1 a custom built system with two 64-bit AMD Opteron (2.0 GHz) processors, 4 GB main memory, 200 GB of mirrored disk storage. This system acts as a database and web server. The server's operating system is 64-bit Ubuntu Linux. A number of web applications are hosted on this system. (biostatdata.emp.vumc.io)
   1 The department's wiki is hosted on a virtual server provided by VUMC's IT department and managed by the Biostatistic's IT Team (biostat.mc.vanderbilt.edu)

Files on the servers are also backed up on a regular basis using the <nop>TiBS service provided by <nop>ACCRE.

---+++ High Performance Computing

[[http://www.accre.vanderbilt.edu/][Advanced Computing Center for Research and Education (ACCRE)]] also operates a High Performance Compute Cluster that department members can use. See ACCRE's [[http://www.accre.vanderbilt.edu/][web site]] for details.

---+++ Secure File Transfer

VUMC provides a [[http://its.vanderbilt.edu/security/secure-file-transfer][secure file transfer web application]] produced by Accellion that gives the ability to send large files securely.

---+++ Wireless Networking

Vanderbilt operates a variety of wireless networks.  A Wi-Fi Protected Access II (WPA2) network is available for VUMC faculty and staff.  An open network is provided for patients and visitors.  Information about the VUMC wireless network can be found at https://it.vanderbilt.edu/services/network/wireless/vumc-employees.php.

---+++ Cloud File Storage

Vanderbilt University provides a [[Main.BoxComNotes][box.com]] account for each faculty and staff member to store, share, and access files online. Box.com is an "in the cloud" file sharing service much like Dropbox. Each user's account provides 50.0GB of storage.

---+++ Printers

Printing services are provided by 7 color laser printers.  All printers are connected to the VUMC campus network.

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.

---+++ Scientific Environment

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.

---+++ Early Stage Investigators

For early stage investigators, the department provides protected time for developing their research programs including the development of methodologic grant proposals. Especially for these early stage faculty, the department also provides funds for professional travel, collaboration with faculty at other institutions, and for books, journals, and professional fees.

---+++ Biostatistics Core Resource

%INCLUDE{"Main.BCC"}%

---+++ Alfresco Community Edition

The department operates a server that runs Alfresco Community Edition.  Alfresco is an open source Enterprise Content Management that we use for project management tasks.  The server is a secure host and repository for discussions, documents, data, and other materials related to a project.

---++++ Security Statement

The Alfresco server is a Linux server that is maintained with all security updates.

The server exists behind Vanderbilt's firewall which actively scans for known attacks, and suspicious actively is immediately investigated by Vanderbilt's network security team. The iptables do not allow for routing packets, and report and log any suspicious packets and drops all malformed packets (usually due to spoofing). Secure shell connections are allowed on a non-broadcasted non-standard port.

All data uploaded to and downloaded from the Alfresco is SSL encrypted using AES 256 encryption with a TLS using SHA256 with RSA for digital signatures. It is therefore safe to use Alfresco from unsecured wireless connections or other public internet access points. SSL connections are further protected by the following technologies:

   * HTTP Strict Transport Security (HSTS) – This ensures that connections are only ever via encrypted HTTPS, never HTTP.
   * Perfect Forward Secrecy (PFS) – This further strengthens SSL to prevent later decryption of data even in the event that the SSL key is compromised. This precaution is considered essential to prevent third parties intercepting private communications.

The Alfresco server only allows password logins and access to documents is controlled via permissions. Content in Alfresco is secured using granular permissions and role-based security to ensure authenticated users only access the content they’re authorized to. Owners can hide folders or files from specific users, or provide read-only access to certain content. All files and folders can have individual permissions set allowing for precise granular control of content. Permission assignments are made in Access Control Lists (ACLs), which are lists of Access Control Entries (ACEs). An ACE associates an authority (group or user) with a permission or set of permissions, and defines whether the permission is denied or allowed for the authority. Every node has a related ACL. When you create a node, it automatically inherits an ACL from its parent. You can alter this behavior after node creation by breaking inheritance or modifying the ACL. We have disabled guest access. We have integrated Vanderbilt's LDAP system for internal logins, and allow for user/password logins for remote users.
Topic revision: r64 - 21 May 2020, DalePlummer
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