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database.bio is reference software for interpreting human variations.

A human genome contains about 3 billion nucleotides. It is estimated that any two individuals . . .

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Get the most out of your data

Life science, meet computer science.

ABOUT US

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L3 is a young and energetic company where IT talents, renowned professors and top-notch industrial partners like BGI work together to invent and develop the future computing technologies for bioinformatics.

It's never easy to develop state-of-the-art technology which advances genomics analysis. We need biologists who understand the bleeding edge problems in genomics analysis. We need experts who knows how to design advanced algorithms to cope with the problems. We need seasoned IT engineers who know how to put together the right computing architecture for the designed solutions. And perhaps the hardest of all, we need a team of all above-mentioned, who can work together.

L3 is such a team.

We build and deliver bioinformatic solutions
for institutions of all shapes and sizes.

BUSINESS SCOPE

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Business Nature

We are a bioinformatics solution provider specializing in the following areas:

  • Algorithm research and development
  • Application software development
  • IT infrastructure design and implementation
  • NGS Analysis
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Target Customers

Our customer base includes NGS service providers, hospitals, pharmaceutical companies and academic research institutions.

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Vision

To become the leading bioinformatics solution provider in Hong Kong and Mainland China, offering IT solutions (including but not limited to algorithms, application software and infrastructure) and NGS analysis services.

To provide its customers with frontier technologies to advance the application of genomics in their services, business or research.

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Mission

Together with its customers, L3 will enhance the world’s understanding of life and lift up people’s health.

Change the way you work. Forever.

PRODUCTS

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database.bio

database.bio is reference software for interpreting human variations.

A human genome contains about 3 billion nucleotides. It is estimated that any two individuals have up to 0.4% difference in their genomes, which is equal to around 12 million base pairs. Variations in these base pairs account for all the differences between the two individuals, from their hair color to their health, and chances to get a particular disease. For researchers, identifying the relevant variations from DNA sequencing data is like looking for a needle in a haystack.

database.bio helps clinical practitioners and researchers in genetic diseases to quickly analyze sequencing data and identify the causal variants. database.bio combines state-of-the-art analytical tools and integrated content, and can drill down to a small, targeted subset of compelling variants based upon published biological evidence and one’s own knowledge of disease biology.

Main Features

  • A user-friendly interface with annotations gathered from 20+ public databases (like ClinVar, OMIM, COSMIC, Orphanet, Drugbank, PubChem, MeSH, SwissProt Pathogenic Variants)
  • Browser supporting the view of human genes (functional protein domains and crystallography)
  • HGVS nomenclature compliant
  • Calculate functional impact of variants with prediction tools:
  • Missense prediction (CADD, Align GVGD, SIFT, MutationTaster, LRT, PolyPhen-2)
  • Nucleotide conservation (GEPR, phastCons, PhyloP, SiPhy)
  • Splicing prediction (GeneSplicer)
  • Regulatory feature prediction (Experimentally Validated TFBS, UniProt Post Translational Modifications, miRBase, CpG Island)
  • Mutation reporting with pathogenicity clues
  • Pharmacogenomics knowledge with Disease, Drug and Clinical Trial details
  • Accessing 1000G, TCGA, ICGC and LOVD resources
  • BAM and BALSA1 alignment viewer with VCF support

Other Features

  • Interactive Pathway annotation using KEGG
  • Common mutation filtration using dbSNP and EVS
  • Pharmacogenomics study by gene to gene interaction
  • Orthologous alignment of multi-species
  • Manages and visualizes variants of multiple samples
  • PubMed abstracts for Variants, Genes, Diseases, Drugs and Pathways
  • Uses standard bioinformatics file formats (e.g., VCF, MAF)
  • Integrating rapid secondary analysis software BALSA1
  • Integrating annotations from HGMD® Professional2, GenomeTrax™2 (BIOBASE)
1 BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU. PeerJ 2:e421
2 Professional license must be purchased from BIOBASE by customers
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BALSA

BALSA is an integrated solution for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 h to process 50-fold whole genome sequencing (750 million 100 bp paired-end reads), or just 25 min for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses. BALSA is published in PeerJ with DOI 10.7717/peerj.421, with a 60 pages user manual. BALSA 1.0’s execution binary is available here.

Version 2.0 new features:

  • Supporting Ion-Proton data.
  • Supporting reads with length up to 500bp.
  • Detecting structural variation.
  • Optimized for multi-socket servers.
  • Modified algorithms optimized for Ampilcon sequencing mode, which is now prevalent in clinical context.

Hardware and software requirements to run BALSA:

General requirements:

  • CPU: Intel or AMD with ≥ 6 cores.
  • Hard drive: 20GB temporary space, 200M SNAPSHOT for a 100-fold human exome. 300GB temporary space, 10G SNAPSHOT for a 50-fold whole human genome.
  • Memory: 32GB for exome. 64GB for a whole genome.
  • GPU: nVidia Kepler, Maxwell architecture with ≥ 1536 cores and ≥ 3GB on-board graphical memory.
  • Operating system: Linux kernel ≥ 2.6.32.
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We are dedicated to tackling challenge every day.

Team

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Tak-Wah Lam, PhD
Co-founder & Board Chair
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David W.L. Cheung, PhD
Co-founder & Director
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Yingrui Li
Director
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Lin Fang, PhD
Director
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Patrick K.C. Yee, PhD
General Manager
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Jeanno C.L. Cheung
Senior Software Engineer
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Jonathan K.K. Tan
Senior Software Engineer
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Katie C.K. Lo
Software Engineer
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Jam Z.Y. Lin
Software Engineer Trainee

We’re passionate about improving lives.

CAReers

Currently, we have multiple openings for Scientific Staff, Software Engineers and User Experience Designers.

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Scientific Staff

Requirements:

  • PhD degree in Computer Science with good publication record;
  • Fresh PhD graduates welcomed; working experience in non-academic post preferred;
  • Preferred research areas: data mining, machine learning, algorithms, system;
  • Prior background in bioinformatics NOT required.

Job Description:

  • To participate in research projects on developing advanced computing technologies for bioinformatics

Monthly Salary:

  • HK$ 27,500 to 45,000, depending on qualification & experience

Should you be interested please send your CV to
recruit@L3-Bioinfo.com

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Software Engineers

Requirements:

  • Bachelor degree in Computer Science or equivalent;
  • Fresh graduates welcome for junior posts; 3 years’ working experience for senior posts;
  • Good teamwork and problem solving skills;
  • Willingness to learn new technologies;
  • Prior background in bioinformatics NOT required.

Job Description:

  • To participate in R&D projects on cloud, database and/or high performance computing technologies

Monthly Salary:

  • HK$ 17,500 to 35,000, depending on qualification & experience

Should you be interested please send your CV to
recruit@L3-Bioinfo.com

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User Experience Designers

Requirements:

  • Bachelor degree or diploma in a designed-related discipline or equivalent;
  • 1 year experience in web design;
  • Good knowledge of user experience design and interaction design;
  • Proficiency in Adobe Illustrator and Photoshop;
  • Knowledge of HTML5, CSS3, Javascript and JQuery is a bonus;
  • Good teamwork and problem solving skills;
  • Prior background in bioinformatics NOT required.

Job Description:

  • To participate in R&D projects; specifically, to produce optimal user experience design for the user interface of the project deliverables

Monthly Salary:

  • HK$ 17,500 to 25,000, depending on qualification & experience

Should you be interested please send your CV to
recruit@L3-Bioinfo.com

Let’s chat!

Our Office

Get directions on a map

13, 21/F, Hong Kong Plaza, 188 Connaught Road West, Hong Kong

For Support

Or any general information

Email:  info@L3-bioinfo.com
Phone: +852 3583 4920
Fax: +852 3583 4921

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