Resources

Spotlight
 
 

Cloud Seq
Unique blend of Next-Generation Sequencing & Cloud Computing technologies
 

Cloud Seq is an innovative platform that makes Next-Generation Sequencing (NGS) projects easy to run and manage without clients needing to purchase expensive sequencing instruments or computer hardware. With absolute transparency, security and confidentiality, Cloud Seq aims to be your trusted research partner for all your sequencing projects.

We are proud to launch Cloud Seq in Singapore starting in January 2013. Initially, we will offer sequencing technologies from both Illumina and Pacific Biosciences. A third option using Ion Torrent from Life Technologies will be made available shortly. All our services come with comprehensive bioinformatics support.

KOOPrime is Singapore's FIRST Next-Generation Sequencing service provider to offer the Pacific Biosciences PacBio RS platform.

We want to offer a one-stop solution for all NGS services in Singapore and Asia.

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Track Record
Highlights of the innovations at KOOPrime which advanced State-of-art for Healthcare and Life Sciences
 

First in Asia to deliver a Genomics Based Heart Diseases Prediction System for Novena Heart Centre and National University of Singapore

First in Singapore to lead Robotic Medical Team, a robotics initiative involving research organizations, hospitals and manufacturers to cater for the needs in hospital and home settings

First in Asia to deliver a fully web based Biodiversity and Environment Database Management System for Singapore National Parks Board

Jointly worked with Singapore Clinical Research Institute, Duke-NUS and National University Hospital Singapore to deliver world first Infectious Disease Clinical Trial Platform and successfully published findings at The Lancet

Secured support of Singapore Prime Minister Office, Singapore Agri-Food Veterinary Authority of Singapore and Eu Yang Sang International to develop the global first Integrated Good Agronomics Traditional Chinese Medicine Electronic System for food safety and traceability purpose

Possibly the first globally to deliver a fully web based Chemical Safety and Traceability System for sharing of protocols and documents for about 100 laboratories at Singapore Polytechnic

Joint development of a global Dengue Surveillance Portal with Novartis Institute of Tropical Diseases

Possibly the first globally to deliver a Animal Facility Management System that can support more than 15000 tanks of fishes at Biopolis, Singapore

Asia first successful DNA Sequencing Data Management System that manages Palm Oil data at Malaysia Palm Oil Board

Possibly the first globally to deliver a DNA Sequencing Data Management System that can support more than 3000 users at Biopolis, Singapore

Joint development of Asia first DNA Oligo Probe Design and Management System with Novusgene Inc, Japan

Asia first successful National Health Data Exchange prototype riding on Health Level 7 version 3.0 standards with Singapore Ministry of Health

Development of Asian Intelligence Management System for usage across 13 countries with Pharmacia

Deployment of Asia first DNA Microarray Fabrication and Analytical System at Singapore National Cancer Centre

Deployment of Asia first High Throughput Screening System to manage 400,000 extracts library at Centre for Natural Products Research

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Infectious Diseases Clinical Data Management Platform
Chloroquine for influenza prevention: randomised, double-blind, placebo controlled trial
 

This is possibly the world first cloud based clinical database, data management and analysis system that alllowed 1500 subjects to take part in an infectious disease study.

A randomised, double-blind, placebo-controlled trial done at a single centre in Singapore. Healthy adults are randomly by system to receive chloroquine phosphate for 1 week or matching placebo by use of a computer-generated randomisation list. Participants fi lled an online symptom diary every week, supplemented by daily diaries and self-administered nasal swabs when unwell. Haemagglutination-inhibition assays for influenza A (H1N1, H3N2) and B were done on blood samples taken at baseline and after 12 weeks. The primary outcome was laboratory-confirmed clinical influenza defined by specific symptoms accompanied by influenza RNA on nasal swabs or a four-fold increase in haemagglutination-inhibition titres over the 12-week study period. Data captured are exported from system for detailed analysis.

A paper on the findings is subsequently published on The Lancet.

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iTrials-HOPE
Integrated Clinical Research Platform for Hepatitis B Cohort Studies
 

iTrials was recently put through a series of successful tests and deployments at the Centre for Molecular Medicine / National University Hospital. The purpose is to study 5000 to 10,000 Hepatitis B subjects over a period of 5 to 10 years.

iTrials is positioned to satisfy growing needs of clinicians, CROs and pharmaceuticals for clinical trials, personalized medicine, drug studies, epidemiological studies, call center management, laboratory results collection, etc. As what Dr Aung Myat Oo, senior research officer ASTAR mentioned, the system is a state of the art system which can handle patients' clinical data intelligently for clinical care as well as sample management for research. As HOPE study database manager & professional advisor during the development, it is a dream come true.

To facilitate efficient management of subjects and samples, various clinical processes are streamlined and automated via the following modules: Questionnaire Module - This allows setting of questions in English, Chinese and Malay. If required, an expert system can be attached to generate summary of findings.

Subject Recruitment & Appointment Module. This is to manage call centers to contact subjects and assign visit dates. The module also verifies the quota of subjects for a day and allows further web based filing of questionnaires.

Subject Registration Module. This includes Pre-screening assignment of subjects. Search functions are provided to verify particulars of subjects.

Subject Screening Module. This includes HL7 components to collect data from existing LIMS systems. It also includes software agents that can directly collect data from instruments so as to facilitate ‘real time’ analysis. This module facilitates Good Laboratory Practices.

Protocols Management Module – This is an intelligent system that can assign protocols for subjects, depending on the conditions of the subjects. The system allows customization of protocol parameters for reminder and alert purposes.

User Management. to control read, write access of different types of users.

The iTrials team has to leverage on expertise and components developed over the past 6 years of clinical focus to ensure successful delivery. The track record includes HL7version 3.0 Message Exchange Prototyping with Ministry of Health (2001), Tissue Management System for Tan Tock Seng Hospital (2002) and Clinical Decision Support System at National University Hospital (2004).

KOOPrime are now exploring opportunities with various CROs and hospitals to facilitate many of the clinical trials that are coming up across Asia.

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BIO-IMSS
Integrated Pipeline Against Infectious Diseases
 

Infectious diseases and epidemics such as influenza and avian bird flu plagues many parts of the world, killing hundreds of thousands to millions. An unpredictable pandemic could kill millions more. Such impact often could not be felt until it is too late, such as the Severe Acute Respiratory Syndrome (SARS) which kept health experts on their toes, fearing when the next major bug will hit.

The Biological Integrated biolaboratory Manufacturing and Services System (BIO-IMSS) was conceived to stop epidemics like the SARS, from ever becoming pandemic. The ingenious idea was conceived by a team of local industry experts from various disciplines from life sciences, to IT and manufacturing) notably, Prof. Robert Gay, A/Prof. Tan Tin Wee, Dr. Dor Ngi, and Mr Lim Teck Sin. The goal is to deliver a one stop, end-to-end disease detection system that will empower health authorities to quickly identify the disease and eventually deploy a detection kit for the disease.

Current collaborators for the BIO-IMSS project includes, National University of Singapore, MC3, National Grid Organization, NovusGene Inc (Japan), Attogenix, Proteus and KOOPrime.

The BIO-IMSS proof of concept was presented at the recent GRID Asia 2005 to Minister for Trade and Industry, Mr Lim Hng Kiang. The IMSS clearly displays how it can autonomously facilitate disease detection through rapid, systematic, biological detection experiments to bio-manufacturing. Integrated over grid computing, the process is further accelerated by grid-enabled bio-instrumentation services. This is important for rapid design and fabrication of diagnostic kits in the event of major outbreaks.

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Sequencing Discovery Platform (SDP)
 

The genomics revolution has opened up exciting new avenues for discovery, but at the same time unleashed a tidal surge of data that continues to overwhelm life sciences researchers. There is a need for a robust, scalable solution that can address various scientific workflow processes, manage the massive data generated from the instruments and elegantly display the results. Such a unique and flexible platform that integrates and streamlines domain workflows in genomics research was recently implemented at Malaysian Palm Oil Board (MPOB).

The Sequence Discovery Platform (DSP) of iBioSuite significantly increases productivity and efficiency of the sequencing labs by integrating and automating sequencing workflows with advanced bioinformatics and data visualization tools. The end-to-end capability gives research laboratories the ability to implement streamlined solutions for the increasingly complex challenges associated with producing, storing and analyzing large volumes of DNA sequence data. It was conceptualized and designed to address bottlenecks in genomics research, especially to leverage information gained from expressed sequence tags, gene and SNPs discovery, as well as for vector sequencing for construct validation.

The iDNAs processes the chromatograms generated from DNA sequencers; automatic quality checking, vector masking, vector trimming, sequence assembly, and passing the processed chromatogram into a designated secure database. Subsequently, the sequences are subjected to a pipeline of homology searches and annotated accordingly. The iDNAs also auto-generates files for sequence submission to databases like GenBank and dbEST. As a result of such end to end integration and automation, more data can be consistently produced and meaningful scientific results also can be easily and securely shared with their colleagues and collaborators worldwide.

KOOPrime has integrated three DNA sequencers at MPOB and demonstrated great improvement in performance. The capacity has surpassed 3,000 daily inputs and serves approximately 50 researchers. This is a critical threshold measurement of its ability to handle very large quantities of data in processing, managing and analyzing DNA. The system is highly-scalable to accommodate to the MPOB Genome Sequencing project in the near future. This potentially involves many more complex integration of analysis applications, including Gene Ontology and Visualization tools for enhanced interpretation of analyzed results.

The result is a successful implementation that streamlines the following processes:

  • Distributed data collection and management of DNA samples over the web.
  • Automated monitoring of the sequencing status of machines on behalf of administrators.
  • Secured publishing of sequence results on the web portal without administrator’s intervention.
  • Updating of sequencing process by a messaging system to inform users about the sequencing system status.
  • Downloading of sequencing results by users through web-based ad-hoc queries.
  • Managing and tracking of expensive resources that are utilized in the sequencing process.
  • Generating of periodic reports for administrators to track the jobs done.
  • Generating of audit logs to track the proper execution of the services.

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