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Tin-Lap Lee: CBIIT GigaGalaxy: A Galaxy-based platform for large-scale genomics analysis
1. CBIIT GigaGalaxy – A Galaxy-based Platform
for Large-scale Genomics Analysis
Tin-Lap, LEE
School of Biomedical Sciences,
CUHK-BGI Innovation Institute of Trans-omics,
The Chinese University of Hong Kong,
Hong Kong SAR, China.
2. CBIIT
• Jointly established between
The Chinese University of
Hong Kong (CUHK) and BGI.
• “We aim to provide a
platform conducive to
training of multi-disciplinary
talents conversant with the
knowledge and application
of genomics, proteomics,
genetics , computation
biology and bioinformatics,
by capitalizing on both
institutions’ expertise and
strengths in genomic
science.”
7. CBIIT GigaGalaxy
Highlights:
• Provides enhanced functionality in additional to the original Galaxy
functions
Specialized instances
Speed: local servers with SBS-UCSC genome database mirror in Hong
Kong
Reproducibility: Seamless integration with Taverna/myExperiment
workflows
Data exchange and publishing: GigaScience journal portal/GigaDB
Customized functions and more…..
8. CBIIT GigaGalaxy
Benefits:
Simplifies complicated bioinformatics tasks, accelerate data processing and
allow flexible analysis.
Significantly reduce software and hardware costs, encourage research
collaboration.
11. What is SOAP?
• SOAP - a tool package that provides full solution to NGS data analysis by BGI.
http://soap.genomics.org.cn/
12. Why SOAP?
• Galaxy has been using SAMtools for consensus sequence calling, but the
recent upgrade has left this part out, which is very limited to some
biologists.
• SOAPsnp is the only other method that can call full consensus sequences
besides SAMtools.
• The main galaxy site supports none of the SOAP tools, including SOAPsnp.
13. Galaxy Tool Shed
• Enables sharing of Galaxy tools across
Galaxy servers around the world.
• SOAP package tools configured for use in
Galaxy.
– SOAPsnp/SOAPdenovo
21. How does it work?
• myExperiment -a repository for workflows.
Taverna workflows.
New: Galaxy workflows.
• CBIIT GigaGalaxy integration
http://www.myexperiment.org
34. 40 Datasets with DOI®s
Invertebrate Released pre-publication
Ant Vertebrates Non-BGI
- Florida carpenter ant Giant panda Paper in GigaScience
- Jerdon’s jumping ant Macaque
- Leaf-cutter ant - Chinese rhesus Plants
Roundworm - Crab-eating Chinese cabbage
Schistosoma Mini-Pig Cucumber
Silkworm Naked mole rat Foxtail millet
Parrot Pigeonpea
Penguin Potato
Human Sorghum
Asian individual (YH) v1+v2 - Emperor penguin
- DNA Methylome - Adelie penguin
- Genome Assembly Pigeon, domestic
- Transcriptome Polar bear
Coming soon…
Cancer (14TB) Sheep
Microbiome data
Hep B infected exomes Tibetan antelope
Single Cell Bladder Cancer Microbes
Ancient DNA E. Coli O104:H4 TY-2482
- Saqqaq Eskimo Cell-Line
- Aboriginal Australian Chinese Hamster Ovary
Mouse Methylomes
36. How are we supporting data
reproducibility?
Data sets
GigaScience
paper Analyses
Community tools for
data reproduction and reuse
37. CBIIT GigaGalaxy
Big data
from the
Data, Data, Data… “Sequencing
Coal Face”
Data
Modeling
Pipeline
design
Tin-Lap Lee, CUHK
Validation
Applications
38. Acknowledgements
• Lee Lab (CUHK) • myExperiment
– Huayan Gao – Finn Bacall
– Dave De Roure
• GigaScience
• NBIC
– Scott Edmunds
– Kostas Karasavvas
– Peter Li
– Tam Sneddon
• BGI-Hong Kong BGI-Shenzhen
– Dennis Chan - Ruiqiang Li
- Ruibang Luo
– Edmond Leung
- Haofu Wu
- SOAP team members
• Galaxy team
– Nate Coraor
The first section of this talk is about implementation of public instance using galaxy tool shed. We are currently implement the first public SOAP instance to the platform.
The SOAP package provides a set of tools for processing NGS data. There are different versions of SOAP for mapping short reads to reference sequences. There are also tools like soapdenovo for construction of a new genome sequence and soapsnp which can assemble a consensus sequence and identify SNPs present on it in relation to a reference. Documentation in the BGI SOAP package is limited in scope, making the tools difficult to use. We will be working with the BGI developers in providing test data and Galaxy pipelines demonstrating the use of SOAP.
Other than its popularity, another main reason to implement SOAP tool is that …
We transform the command line base SOAP tool into galaxy instance by Galaxy tool shed. The tool shed is useful to transofrm any programs through python rapper. I should say the Galaxy team did a great job on this, and they are very helpful during the development process. By doing that.. It allows
You can notice that all the parameters has been transformed into drop-down menu..We also put an explanation for each par. So that the user has a better understanding on each item.
Similar to SOAPsnp, the complicated parameters or option has been transformed. The settings will be recorded in each run, so that one can track back easily.
So much for the tool development, the second part of the talk will focus on work flow implementation using the workflows from myexperiment.
What does semantic mean in the
Introduction into GigaScience, a journal published by BGI and BioMed Central which focuses on the publication of papers involving the analysis of large-scale omics data - show first issue slide. In addition, the journal has a focus on enabling the experimental data and results published in its papers to be reproducible for readers. Data produced from post-genomic experiments can be stored in GigaScience'sGigaDB database. It currently holds 37 data sets of mainly NGS data - show slide. Each data set is allocated a DOI - Digital Object Identifier which enables the data set to be uniquely identified and used for its citation, providing a handle for tracking its usage.