Wake Forest Baptist Comprehensive Cancer Center (Director: Boris Pasche, M.D., Ph.D.)
The main campus facilities of the Wake Forest Baptist Comprehensive Cancer Center (WFBCCC) (Figure 1) are well-defined and include the new Cancer Hospital and WFBCCC administrative space [A], as well as WFBCCC laboratories for basic sciences and Shared Resources [C, D, E, G]. Other facilities include substantial space in the Wake Forest Innovation Quarter (Figure 2) (Biotech Place [20]; 525@Vine [21]; the Dean Building [6]); Piedmont Plaza; the Reynolda (WFU College of Arts and Sciences) Campus; and the Clarkson Campus (Wake Forest Primate Center). These are accessible via a shuttle service that runs throughout the day from the main Medical Center Campus.
Figure 1. WFBCCC main campus facilities. (A) WFBCCC inpatient and outpatient Cancer Hospital; (B) Brenner Children’s Hospital; (C) Gray Building; (D) Hanes Building; (E) Nutrition Research Center (NRC) Building; (F) Watlington Hall; (G) MRI Building.
Oncology Outpatient Facilities
The outpatient facilities are located on the first four floors of the WFBCCC building (Figure 3a and b) and provide state-of-the-art care for cancer patients. They include multidisciplinary clinics, the Clinical Protocol and Data Management (CPDM) nurses and data managers, Radiation Oncology, the WFBCCC’s Cancer Patient Support program, diagnostic radiology, and mammography suites.
Figure 3a. WFBCCC Outpatient Floors
Figure 3b. WFBCCC Outpatient Floors
Oncology Inpatient Facilities
Inpatient clinical activities in adult medical, gynecologic, and surgical oncology are consolidated in the new WFBCCC hospital with 148 inpatient oncology beds, including a twenty-bed specialty care Bone Marrow Transplant Unit on the seventh floor and a dedicated oncology intensive care unit on the eighth floor. The pediatric oncology program is located in the adjacent Brenner Children’s Hospital, which is contiguous to the new WFBCCC building (Figure 4).
Administrative offices
Figure 4. WFBCCC Inpatient Floors
The new WFBCCC building offers additional office space and markedly expands conference capabilities with the addition of three state-of-the-art conference rooms (Figure 5). The tenth floor also houses the central pharmacy, including chemotherapy preparation for both adult and pediatric patients, and the Investigational Drug Service. In addition, WFBCCC Clinical Protocol and Data Management regulatory and finance operations are located on the tenth floor. The eleventh floor is occupied by the Director and the administrative team, as well as the Cancer Service Line and additional space for Biostatistics and Informatics personnel. Radiation oncology faculty members have offices on the first floor of the WFBCCC Cancer Hospital building. Administrative offices for other WFBCCC clinical faculty members are located in Watlington Hall (refer to Figure 1), which is directly connected to the WFBCCC Cancer Hospital.
Figure 5. WFBCCC Administrative Floors
Clinical and Population Science Programs
Oncology Departments and Sections
The Wake Forest School of Medicine is comprised of 37 clinical departments, including the sections on Hematology and Oncology, Radiation Oncology, and Surgical Oncology.
Hematology and Oncology: Bayard Powell, M.D., WFBCCC Associate Director for Clinical Research, is chair of the section on Hematology and Oncology. Major areas of clinical research activity include leukemia and hematologic malignancies, breast cancer, colon cancer, and prostate cancer. A comprehensive bone marrow transplant program has been developed that includes trials utilizing both autologous and allogeneic bone marrow transplantation. The joint Hematology and Oncology Fellowship program, led by Susan Melin, M.D., Clinical Research Program member, is a three-year program leading to ABIM Board eligibility in Medical Oncology and Hematology. In addition to the inpatient and outpatient rotations at the WFBCCC, fellows rotate at the W.G. (Bill) Hefner VA Medical Center in Salisbury, NC.
Radiation Oncology: William Blackstock, M.D., WFBCCC Clinical Research Program Leader, is chair of Radiation Oncology. The Radiation Oncology department participates in and conducts multidisciplinary research in Translational Radiation Oncology, Radiation Biology, and Radiation Physics. Radiation Oncology is an accredited four-year residency training program by the Accreditation Council for Graduate Medical Education. The Radiation Oncology department also provides graduate-level education for Ph.D. candidates in the joint Virginia Tech – Wake Forest University School of Biomedical Engineering and Sciences.
Surgical Oncology: Edward Levine, M.D., The chair of the section on Surgical Oncology is a Clinical Research Program member. The section on Surgical Oncology, within the Department of General Surgery, performs over 1,500 major operative procedures annually and participates in research related to surgical treatment of malignancies of the breast, head/neck, gastrointestinal tract, liver, biliary structures, pancreas, melanoma, and sarcoma. The Section offers a two-year surgical oncology fellowship, led by Clinical Research Program member Perry Shen, M.D., to fully-trained general surgeons who desire advanced training.
Figure 6.
Pediatric Oncology: Thomas McLean, M.D., The pediatric hematology and oncology program at Brenner Children’s Hospital is led by Dr. McLean who is a Clinical Research Program member. The pediatric oncology team is comprised of pediatric hematologists and oncologists, pediatric surgeons, and radiation oncologists who contribute to pediatric research advancements in cancers of the bone and soft tissue, leukemia, and lymphoma. WFBCCC members are Drs. McLean and Russell.
WFBCCC members also have clinical appointments in the departments/sections of Gynecologic Oncology, Neurosurgery, Otolaryngology, and Urology. All WFBCCC patients are seen and treated at the Cancer Hospital, Brenner Children’s Hospital, or one of the WFBCCC satellite community clinics (Figure 6).
Wake Forest NCORP (NCI Community Oncology Research Program) Research Base
The Wake Forest NCORP Research Base (U10CA081851; PI: Lesser) is a research base for cancer center affiliates and for NCI-funded NCORP Community Sites (Figure 7). WFBCCC is the only NCI-designated Comprehensive Cancer Center with an NCORP Research Base. NCORP designs and conducts cancer prevention, control, screening, and post-treatment surveillance trials; conducts cancer care delivery research, including comparative effectiveness research; and integrates disparities research questions into clinical trials and cancer care delivery research.
This program provides a conduit for community physicians to participate in NCI-supported trials, giving their patients enhanced access to high-quality research studies in their own communities. Glenn Lesser, M.D., (PI, Co-Leader of the Clinical Research Program) and Kathryn Weaver, Ph.D., (Co-I, Co-Leader of the Cancer Prevention and Control Program) lead the WF NCORP Research Base. WFBCCC members Drs. Danhauer (CPC), Klepin (CRP), Rapp (CRP), and Vitolins (CPC) serve on the Executive Steering Committee.
Figure 7. NCORP Community Sites
Office of Cancer Health Equity (OCHE)
The OCHE is a partnership with the Maya Angelou Center for Health Equity. The two Centers jointly fund a Community Engagement Coordinator to integrate efforts in developing and implementing research and educational programs specifically for underserved communities in the WFBCCC catchment area. The OCHE seeks to enhance understanding of the needs of underserved patients in the WFBCCC catchment area, remove barriers to care for underserved populations, increase diverse participation in clinical trials, and facilitate community engagement to improve outcomes. It is led by the Director for Cancer Health Equity, Karen Winkfield, M.D., Ph.D., Associate Director Jimmy Ruiz, M.D., and Assistant Director, Kathryn Weaver, Ph.D. The OCHE is supported by a Program Manager, Community Engagement Coordinator, Hispanic Clinical Trial Navigator, Community Health Educator, and a Cancer Health Equity Advisory Group.
Basic Science Programs, Research Labs, and Shared Resources
A total of 121,861 sq ft of laboratory space, with 81,377 sq ft in use (December 2015) and 40,484 ft available for new recruits, is assignable by the WFBCCC Director. Most of the WFBCCC laboratory space is located on the main medical center campus. Two research buildings in the Innovation Quarter (Figure 2) house Cancer Center investigators: the Richard Dean Building and Wake Forest Biotech Place (opened in 2012). This includes an interdisciplinary mix of investigators from Biochemistry, the Virginia Tech–Wake Forest University School of Biomedical Engineering and Sciences, Cancer Biology, Microbiology and Immunology, and the Institute for Regenerative Medicine. Shared Resources, such as the Crystallography and Computational Biosciences and part of the Flow Cytometry, are also located at Wake Forest Biotech Place.
Computational Informatics Resources
A variety of computational platforms are available for faculty and staff to perform their research activities. These range from interactive Linux systems used for primary statistical and genetic analysis, to high-performance computing clusters used for distributed parallel processing, as well as Windows-based servers used for database and statistical processing. Details are provided below.
Core Interactive Systems: (2) Linux Servers – IBM BladeCenter nodes with 8 Dual Core Xeon 2.40 GHz CPUs, and 98 GB RAM, each
High-Performance Computing Clusters (HPCC): The high-performance computation facilities include a) 23 Node / 92 core IBM Blade cluster, 828GB RAM; b) Access to 140+ Node / 482 core IBM Blade cluster – “DEAC Cluster”, with a combined 2.8TB RAM (see more details below); c) DEMON-Isilon (1,358 2.6GHz Intel CPU cores, 4,992 706MHz Nvidia GPU cores, and 190 TB parallel storage space).
Wake Forest University DEAC Linux Cluster: The DEAC Linux Cluster has 153 computational nodes dedicated to research and teaching use. These nodes are connected via gigabit Ethernet to six-disk server nodes. The disk server nodes provide a parallel, distributed file-system interface to the fiber channel storage area network (FC SAN). This cluster is managed with four maintenance nodes, through which users access it. The cluster FC SAN is based on a 7TB (usable) IBM ESS 800 storage device. This device has four FC connections to redundant eight port switches. The six-disk servers have dual FC adapters to redundantly attach to the FC switches. Connectivity to the compute nodes is provided by the dual, redundant gigabit Ethernet connectivity to the cluster core network switch. This arrangement provides the highest possible fault tolerance and results in stable environments for compute nodes to access data. The cluster is directly connected to the Wake Forest University campus core network router through fiber-based, gigabit Ethernet.
The cluster, hardware, and software are fully-supported by the Wake Forest University Information Services Department. The WFU DEAC cluster is co-located at a commercial server room facility in the Innovation Quarter, the research park in downtown Winston-Salem, NC. The WFU DEAC cluster is the primary tenant of this server room, measuring approximately 625 sq. ft. with an additional finished 625 sq. ft. expansion capability. At its current configuration, it can support the power needs for cluster growth up to a factor of two in size and the space needs for a factor of five increase in cluster size. Internally, the cluster is capable of significant growth. By design, the cluster scales on all fronts through the simple addition of hardware: computational power scales by adding compute nodes, interactive logins scales by adding head nodes, cluster maintenance requirements scale by adding maintenance nodes, disk bandwidth scales by adding disk nodes to the GPFS file system, disk capacity scales by adding fiber channel based storage to the SAN. One of the most important responsibilities the DEAC/Osiris cluster undertakes is the education of the students at Wake Forest University. Clusters provide enormous computational power to tackle more advanced scientific problems, opening up the possibility for our students to gain a unique perspective on topics in the forefront of research today. Any faculty member can request the use of the cluster for a course. Several courses actively use the DEAC/Osiris cluster to enhance students’ exposure to the advanced computing environment provided by the University.
Central Storage: Each of the systems listed above connects to the centralized storage system, which provides over 130 TB of storage for researchers. Storage platforms include Isilon, EMC, and Compellent. Over forty Windows-based servers are managed for uses including application servers, database servers and file servers. Members of the Department of Biostatistical Sciences have created clinical trials web platforms encompassing database servers, web hosting servers, and SAS servers so that study staff can have real-time access to clinical trial data.
All servers that are available to the Internet are secured in a DMZ zone, with two hardware firewalls. Local software firewalls are also used on each public server. Public server access is monitored at the hardware firewall location, by an outside monitoring company. The Division also monitors public servers, at the server software location, to help guarantee security. Operating system patches and hotfixes are implemented in a timely-fashion, and can be managed remotely in an emergency.
All servers are physically located in one state-of-the-art 5,500 square foot data center, located in the Innovation Quarter. The facility is designed for security and reliability and provides a central presence for high-end computing (e.g., computing clusters), data storage facilities, centralized backup, and disaster recovery. The entire building’s electrical needs are backed by a one Megawatt on-site generator. The data center provides a fully monitored environment for data processing equipment used by faculty at the undergraduate campus of Wake Forest University (WFU) and a collocation facility for commercial and public service providers for the Innovation Quarter, ensuring multiple high-bandwidth Internet paths.
The networking environment is a fully-converged, high-speed, multi-use network supporting video streaming, VoIP, video teleconferencing, and high-bandwidth display signage, in addition to the typical data traffic along with a fully-integrated wireless environment across all campuses. WFU is one of the founding members of Internet II and utilizes the research and education network daily with our shared Virginia Tech – Wake Forest University School of Biomedical Engineering. WFU also provides the Piedmont region of North Carolina with a Regional Point of Presence (RPoP) called WinstonNet. This robust connection to Internet II and to the North Carolina Research and Education network (NCREN) is capable of ten Gbps and is positioned to move to the Lambda Rail.
Databases: Data Lake: WFBMC has established a “Data Lake” platform based on the Pivotal Data Computing Appliance (Pivotal DCA), which is an integrated analytics platform. Pivotal HD supports a complete Hadoop-based processing platform including several Apache distributions such as Spark and other native Hadoop tools. The Data Lake consists of Pivotal Greenplum Database (Pivotal GPDB), Hadoop File System (HDFS) storage, and Hadoop with Query (HAWQ). HAWQ is a parallel SQL query engine that combines the key technological advantages of the industry-leading Pivotal Analytic Framework with the scalability and convenience of Hadoop mainly for unstructured data. Currently, there are 70TB of Hadoop File System (HDFS) storage available and it is being increased to 250TB HDFS (plus 250TB backup) with estimated completion of March 2016. The goal is to create an in-memory computing environment with Apache Spark and MLLib type tools.
Software on Data Lake: WFBMC has purchased the Alpine Chorus, which is a new advanced analytics platform for the enterprise. It creates an open framework to manage the entire analytics lifecycle, from exploring data to operationalizing insights. It allows: a) application development in an agile, secure, visual & web based framework, b) In-cluster technology to run analytics on any data needless to transfer data, c) optimized machine learning algorithms for parallel processing on Hadoop and traditional databases, d) Data science support from discovery to exploration and modeling.
Data Warehouse: WFBMC has implemented the widely adopted informatics for integrating biology and the bedside (i2b2) as a framework for researchers to query the clinical and research data in a compliant manner and the Translational Data Warehouse (TDW) to store clinical and research data sets both of which run on the Data Lake infrastructure. TDW houses de-identified clinical data that includes demographics, diagnoses, procedures, medications, lab results, and other data from the electronic medical record (EMR) and de-identified Cancer Registry data. i2b2 is the cohort discovery tool for researchers to access and utilize data along with the other clinical and specimen data in the data lake. Additionally, the Data Lake and i2b2 are our interface point to external networks such as Guardian Research Network, Foundation Medicine PMEC, SHRINE and mySCHILS (funded by PCORI CDRN).
Software: Members of the Biostatistics and Bioinformatics Shared Resource (BBSR) assisted in the development of Pathway analysis tools, omics integration tools, Next generation sequencing data analysis tools, phosphoproteomics data analysis tools, clinical data warehouse, Cell-IA, itNETZ, DTW (clinical data warehouse), CellIQ, and other in-house image processing software packages, including serial image computing software using C++. In addition, BBSR members and other collaborators have developed novel analysis tools, including Dandelion, which performs case/control haplotype analysis using the EM algorithm; Dprime, which calculates estimates of D, dprime, delta and r-square using independent individuals; and SNPGWA, which is used for genome-wide association analysis, performs linkage disequilibrium measures, tests for Hardy-Weinberg Equilibrium, tests for general association, 3 genetic models (dominant, additive and recessive), tests for lack of fit, performs an allelic test and conducts 2- and 3-marker haplotype analyses using the EM algorithm. The following list comprises a subset of statistical and bioinformatics applications:
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DCMTK
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Gene Hunter
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Glogit
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Ghp
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Haploview
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HRT- Haplotype Runs Test
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Imaris
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IPA
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ITK
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Loki
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Matlab
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Matrox Imaging Library (MIL)
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Mendel
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Merlin
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Mimics
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Non-Parametric Linkage Regression Analysis
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ORACLE
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OSA- Ordered Subset Analysis
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PDT – Pedigree Disequilibrium Test
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Pedcheck
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PedSys
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PHASE
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Prest
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R
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SAS
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Splus
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Slidebook
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Solar
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Structure
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TDK
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Unphased which includes haplotypic PDT and QPDT
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Zaplo/Profiler
See Table 2 below for a list of sequencing software.
Table 2.
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Sequencing raw data processing
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RNA-Seq
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Quality control and filtering
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FastQC, FASTX, HTSeq, RNA-SeQC, BamHash, DeconRNASeq
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Alignment
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Bowtie, Bowtie2, Burrows-Wheeler Aligner (BWA), hts_mappers, Maq, SeqMap, IsoformEx, SpliceSeq, SpliceMap, STAR, TopHat, SpliceR, MAQ
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Normalization Quantitative analysis
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DESeq, Cufflinks/Cuffdiff, EdgeR, GPSeq, RSEM
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Whole genome sequencing and exome sequencing
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Quality control and filtering
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Firehose, Preseq, QC3, ngsCAT
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Sequence alignment
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Picard, Bowtie2, MAQ, BWA
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Base Calling
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BlindCall, Swift, GenePattern
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Variant identification
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SAMtools, Atlas2, GATK UnifiedGenotyper, CANOES, cnvCapSeq, ExomeCNV, BIC-seq, BreakDancer, Meerkat
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Variant annotation
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ANNOVAR, Exomiser
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Mutation significance
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MutSig, MuTect
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Small RNA sequencing
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miRNA analysis
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MicroRazerS, SHRiMP, Tailor, miRNAkey, miRanalyzer, miRDeep, miRExpress, miRTools
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ncRNA identification
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omiRas, miR-PREFeR, miRDeep, miRExpress, segmentSeq
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miRNA binding site
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TargetScan, STarMir, miRanda, PicTar
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ChIP-Seq
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Quality control and filtering
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Phantompeakqualtools, CCAT, htSeqTools
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Sequence alignment
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Bowtie2, MAQ, BWA
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Peak Calling
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MACS, BroadPeak, CSAR, NarrowPeaks, PICS
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Differential Peak Calling
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BEADS, DiffBind, histoneHMM, MMDiff
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Motif discovery
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MEME Suite, HOMER, MEME-ChIP
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Peak annotation
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ChIP-Enrich, ChIPpeakAnno, ChIPseeker, PeakAnalyzer
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Chromatin segmentation
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ChromHMM, Segway
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Sequencing analysis
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Analysis purpose
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Tools
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Data types
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Functional SNPs
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FunciSNP, snpeff, Matrix eQTL
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SNP array or whole genome seq
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Molecular signatures
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Oncotype DX, MammaPrint, Metagene, Rotterdam signature
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Gene Microarray and RNA-Seq
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Copy number variation analysis and cytoband detection
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GISTIC2, Unsupervised clustering, D-ToxoG, HAPSEG, Tumorscape
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SNP array
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Mutation
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Strelka, Indel locator, ABSOLUTE, CHASM, Assessor, APOBEC, Fastbreak, BreakPointer, ChainFinder, Indelocator, Oncotator
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Exon-Seq or whole genome seq
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Alternative Splicing
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JuncBASE, AltAnalyze, MapSplice, SpliceMap, HMMsplicer, Cufflinks, Scripture, Trinity, Trans-ABySS, GRIT, ALEXA-seq, MISO, SplicingCompass, MATS, MISO, casper
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RNA-Seq
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DNA methylation and related-gene identification
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ConsensusClusterPlus, hypermethylation frequency detection, DiffVar, MethylMix
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DNA methylation array
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Microbiome analysis
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hEBV, PathSeq
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mRNAseq
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Integrative analysis
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iCluster, PARADIGM, PARADIGMD_SHIFT, MIRACLE analysis, NMF, PCA, TieDIE, COCA, SuperCluster, RF-ACE, dRanger, GeneCruiser
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Multiple data types
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Visualization
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cBioPortal, UCSC Genomics Browser, Golem, Hukilau, IGV, Heatmap, TCGA Wanderer
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Multiple data types
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Other Systems: The WFBCCC informatics team has access to several IDE/code development software (Visual Studio, Eclipse, etc.) and has recently purchased 1) the Atlassian software development suite that includes following components:
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Jira: Plan, track, and release world-class software with the widely used software development tool for agile teams.
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Confluence: Organizing the development work, create documents, and discuss everything in one place in order to spend less time to find documentation and code.
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Bitbucket and Git: Code collaboration tool with inline comments and pull requests. It also manages and shares Git repositories to build and deploy software.
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Bamboo: Continuous integration, deployment, and release management.
2) The Tableau Software, which contains various interactive data visualization products focused on business intelligence. The WFBCCC is currently expanding reporting system functionality into the Tableau business intelligence platform so that operational and research data can be fed into dashboards for real-time monitoring of key metrics.
Center for Bioinformatics and Systems Biology
The Center for Bioinformatics and Systems Biology (CBSB) provides a bioinformatics infrastructure as well as expertise in systems biology protocol development, high-performance computing, biomedical data storage, and data analysis to assist investigators at Wake Forest University Health Sciences. It is led by Xiaobo Zhou, Ph.D., WFBCCC Co-Director of the Biostatistics and Bioinformatics Shared Resource. The goal of the CBSB is to be a leader in the development and applications of novel systems, bioinformatics methods, and molecular diagnosis, as well as their integration into clinics and disease monitoring. The CBSB has five research laboratories: Bioinformatics, Experimental Systems Biology, Systems Modeling, Biomedical Physics/Imaging, and Big Data Sciences and Clinical Informatics. The CBSB occupies approximately 10,000 square feet and has both dry and wet labs. The dry labs focus on developing advanced computational bioinformatics tools, clinical and translational informatics, biomedical imaging informatics tools, and systematic modeling tools to answer various biological and medical questions related to biomarker and drug-target discovery, drug signature discovery, drug resistance mechanism discovery, disease mechanism, personalized medicine and drug delivery, to improve basic, clinical and translation research and provide bioinformatics and data analysis support for other investigators. The wet lab - experimental systems biology focuses on understanding stem cell niche, immune cell-cell interaction system, data generation and validation.
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