Genomics and Data Analytics Core | Cancer Science Institute of Singapore (CSI)

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Genomics and Data Analytics Core – Cancer Science Institute of Singapore (CSI)

Genomics and Data Analytics Core (GeDaC)

The Genomics and Data Analytics Core (GeDaC) at the Cancer Science Institute of Singapore (CSI) is designed to meet the increasing need of bioinformatics and computational support for institute labs. Its mission is to, 1) provide investigators access to bioinformatics expertise and solutions, 2) use data science to enhance the impact of CSI’s research, and 3) develop innovative platforms for cancer genome analytics.

GeDaC is part of a broader vision to establish CSI as a regional and global leader in cancer-related computational biology.

For further information and to discuss how we may help you with your computational biology work and price list, please contact the Genomics and Data Analytics Core (GeDaC) via email (csi_gedac[at]nus.edu.sg).

Facility Head

Dr. Jason James PITT

Special Fellow, Cancer Science Institute of Singapore, NUS

jason.j.pitt[at]nus.edu.sg

Dr. Touati BENOUKRAF

Visiting Assistant Professor, Cancer Science Institute of Singapore, NUS

benoukraf[at]nus.edu.sg

Dr. Kumaran Kuppusamy MANDE

GeDaC Manager

Senior Research Scientist, Cancer Science Institute of Singapore, NUS

kmande22[at]nus.edu.sg

Service Unit Lead

Henry YANG

Lead of GeDaC Research Bioinformatics Unit

Research Associate Professor, Cancer Science Institute of Singapore, NUS

csiyangh[at]nus.edu.sg

Tony TAN

Lead of GeDaC Clinical Bioinformatics Unit

Senior Research Scientist, Cancer Science Institute of Singapore, NUS

csittz[at]nus.edu.sg

Ömer AN

Lead of GeDaC Scaling Unit

Research Scientist, Cancer Science Institute of Singapore, NUS

csioan[at]nus.edu.sg

CK ONG

Lead of GeDaC Storage Unit

IT Manager, Cancer Science Institute of Singapore, NUS

csiock[at]nus.edu.sg

Team Members

Li YING

GeDaC Research Bioinformatics Unit

Research Associate, Cancer Science Institute of Singapore, NUS

csiliyi[at]nus.edu.sg

Juan Felipe ORTIZ QUINONEZ

GeDaC Research Bioinformatics Unit

Research Scientist (Bioinformatician), Cancer Science Institute of Singapore, NUS

jf.ortiz[at]nus.edu.sg

TOH Qin Kane

GeDaC Research Bioinformatics Unit

Research Fellow (Bioinformatician), Cancer Science Institute of Singapore, NUS

kanetoh[at]nus.edu.sg

LINGANESAN Kularatnarajah (Mani)

GeDaC Scaling Unit

Software Engineer, Cancer Science Institute of Singapore, NUS

mani[at]nus.edu.sg

CHIA Yong Keng, Hydrus

GeDaC Storage unit and administration

IT Analyst, Cancer Science Institute of Singapore, NUS

ykchia@nus.edu.sg

Chin Min TOH

GeDaC Genomics Bench and administration

Senior Laboratory Executive, Cancer Science Institute of Singapore, NUS

tcm[at]nus.edu.sg

Services and Solutions

GeDaC is providing services and solutions made up of three collaborative and complementary units as illustrated below.

Services

We provide services for 1) project-based consultation and analysis for research groups , 2) best practice pipelines for common genomic data (e.g. NGS) processing and analyses, 3) standardization and storage of CSI datasets, and 3) sequencing library preparation.

The facility also houses CSI’s Genomics Bench that is equipped with a variety of equipment to support research analysis within the institute. The full list of equipment under the Genomics Bench are:

Illumina NextSeq 500
Illumina MiSeq
10x Genomics Chromium Controller
Agilent 2100 Bioanalyzer
Agilent 4200 TapeStation
Covaris ME220 Focused-ultrasonicator
Diagenode Bioruptor Plus
Diagenode Bioruptor Pico
Bio-Rad QX200 Droplet Digital PCR

Storage/IT

The Storage unit is responsible for the maintenance of CSI servers and storage management such as backup and archiving. The unit also provides support for the institute’s cloud computing transition, security, and network maintenance.

Scaling

The Scaling unit provides support and assistance to users on how to transform bioinformatics pipelines into scalable and portable workflows. The unit is also developing a cloud-based software stack to harmonize/warehouse local and public sequencing data. This includes constructing modern APIs/databases to facilitate smooth data access for CSI researchers. Finally, this unit will liaise with tech industry partners as well as manage collaborative efforts between CSI and the Genome Institute of Singapore.