Data Loading...
Invoice (1) Flipbook PDF
Invoice (1)
114 Views
12 Downloads
FLIP PDF 1.7MB
BIOINFORMATICS SIMPLIFIED
Intelligent Design For Genomics Applications
Stanome - Vision and Mission ● Stanome is an enterprise cloud bioinformatics solutions company offering a turn-key, cost-effective cloud computing platform for genomics applications and analysis ● Democratize genomics applications development with a one-stop solution for data storage, security, provenance, and reproducible data analysis ● Bioinformatics data analysis and applications platform • Empowering scientists through driving innovation • Accelerate genomics research and reduce the time it takes to make life-changing discoveries • Generate more value out of genomics data
BIOINFORMATICS SIMPLIFIED
A Platform With Intelligent Design For Increasing Productivity Provide free data quality report for every sample. Final reports are comprehensive and readily publishable
Project setup to pipeline execution in less than five minutes
Secure Data Sharing
Reproducible and accurate results with comparative analytics from multiple pipelines
Differentiates and pairs Single End (SE) and Paired End (PE) sequencing data files, selects commands and sends status updates
Application Development
Cloud-based web application
Data Visualization
Faster Data Upload
Based on project setup, genome, transcriptome and annotation files are automatically selected
Data Analysis
Execute pipelines for any organism through custom reference(s) and indexing without user intervention BIOINFORMATICS SIMPLIFIED
Built on AWS Cloud Capabilities Serverless architecture scales computing resources on demand, hence no need to wait in the queue
Pay only for what you use without minimum mandatory service usage
Automatic re-executions of the pipeline
Optimized Costs
Cloud Failure Detection
Serverless Computing & Auto Scaling
VMs are selected based on the tool - helps to optimize the costs Dynamic VM Selection
Multi Tenancy
Data segregation with private virtual cloud and group sharing BIOINFORMATICS SIMPLIFIED
Creating Value @ Each Step of Platform Usage
❖
❖
We offer a simple end-to-end workflow in five easy steps, which takes less than five minutes of hands-on time. Automation behind each step lets users interact with the platform effortlessly.
Data Upload
• Upload samples to DataStore only once • Custom references are allowed • Hassle free sample pairing
Project Creation
• Create a project and define the objectives using drop-down menus • No confusion of selecting any other file(s)
Sample Inclusion
• Select samples from Data Store • The platform provides guidance to minimize errors in sample selection
Pipeline Selection
• Select pipelines based on data type and analysis requirements • Utilize pre-built pipelines or create de novo • No command editing for Single End and Paired End samples
Execution
• Execute pipelines with one click • Receive email notifications of job progress and status • Final report and ALL intermediate files are readily available BIOINFORMATICS SIMPLIFIED
Faster Upload and Analysis Timelines Platform
Upload time ( 3 GB compressed files)
Stanome
16 min
Basepair Tech
3 hrs.
Galaxy
20 min
Onramp
40 min
Less than FIVE minutes of hands-on time Project Setup
Sample Set
Select Pipeline
Execution & Monitor
One hour sample-to-results time* * Based on a eight sample Paired End (PE) RNA-seq data ( ~ 80GB raw data) BIOINFORMATICS SIMPLIFIED
Pipelines are Organized Into Hubs
TranscriptHubTM
MicroHubTM
VariantHubTM
• Differential Gene Expression • Fusion, Splice Junctions and Transcript Isoform Identification • De novo Transcriptome Assembly • Pathway Analysis • Functional Annotation and Gene Ontology • Variant Analysis • Prime Pipelines
• Assembly and non-assembly methods of microbial detection • Amplicon (e.g., 16S) Analysis • Shotgun DNA Analysis • Shotgun RNA Analysis • Comparative Genomics and Phylogenetic Analysis • Taxon Assignment • Genome Assembly and Annotation • Antibiotic Resistance Screening
• Genome Quality Analysis • Reference Genome Assembly • De novo Variant Detection (SNPs, INDELs, and Structural Variants) • Case-Control Variant Studies • Family and Cohort Analysis for Personalized Medicine • Genotyping-by-Sequencing (GBS) • Variant Interpretation and Prioritization
SoftwareHubTM
Prebuilt Pipelines Custom Pipeline Design High Throughput Analysis Cloud Computing Platform-as-a-Service (PaaS) • Software-as-a-Service (SaaS) • • • • •
BIOINFORMATICS SIMPLIFIED
Sample Pipeline for Genotyping Application Dynamic Data Upload
Data Cleanup and Quality Report
Automatic Analysis (Mapping & Calling)
Report Genotypes
• Direct data upload from the sequencer to the cloud without human intervention • Provide frequent updates on the upload progress
• Sample demultiplexing, cleaning, and pairing • Provide quality report for each sample
• No need of genome indexing • Mapping, variant calling, filtering, genotype calling for SNPs and INDELs • Industry best practices are implemented using tools such as BWA and GATK • • • •
Genotypes are reported in table formats and can be combined with metadata All intermediate analysis files are available for download Every tool, command and parameters are reported for data provenance Email notification after the analysis completion BIOINFORMATICS SIMPLIFIED
Stanome is Application Focused vs APIs Enablement
Stanome is built on analysis foundation to develop industry specific applications development
Personalized Treatments Gene expression for diagnostics Targeted sequencing for genotyping
Precision Medicine and Agriculture Transcriptomics Exome
Screening for microbial resistance
AMR
TranscriptHub and VariantHub
Hubs
Competitors are building bag of tools (APIs) for data analysis as final solution
Tool Kits APIs
BIOINFORMATICS SIMPLIFIED
Differentiating Feature and Value Proposition Platform Features
Stanome
SevenBridges
DNANexus
Basepairtech
Galaxy
Automatic pairing of samples
Yes
No
No
No
No
Dynamic reference indexing and auto-selection
Yes
No
No
No
Yes
Data-driven command selection
Yes
No
No
No
No
Prime pipelines*
Yes
No
No
No
No
Pipeline building
Convenient
Requires expertise
Requires expertise
Convenient
Requires expertise
Project setup & Pipeline execution
< 5 mins
Requires expertise
Requires expertise
Not possible
Requires expertise
Data upload
Very fast
Requires application installation
Fast
Slow
Fast
Multi-layered reporting**
Available Free Quality Report
Only FastQC report available on demand
Only FastQC report available on demand
Only analysis report available
No
Ease of use
Convenient
Requires expertise
Requires expertise
Convenient
Requires expertise
Pricing
Charges for analysis only; No data storage costs$
Cost for both, storage and pipeline run
Cost only for pipeline run and not for data storage
Cost for both, storage and pipeline run
Free but storage limited to 250GB
$ Data is deleted within a week from the analysis date BIOINFORMATICS SIMPLIFIED
Flexible Models
Model1 Model
1
●
Cloud - Platform-as-a-Service
Model Model2
2
●
Cloud - Software-as-a-Service (Per Sample)
●
Cloud - Software-as-a-Service (Fixed Cost)
●
On-Prem Solution
Model 3
Model Model4
4
BIOINFORMATICS SIMPLIFIED
Business plan and target customers Revenue Model
Research organizations
SAAS Model
PAAS Model
(At least 100% markup on the AWS costs)
(At least 25% markup on the AWS costs)
★ Per sample analysis charges ★ Custom analysis charges
★ B2B license fee ★ Platform usage (analysis) costs ★ Maintenance and support fee
Genomics solutions providers
Clinical trials Lorem and ipsum therapeutics
Target Lorem ipsum Customer congue Segment
Biotech. companies
Academic institutions
Sequencing service labs
Diagnostics companies Genotyping for agriculture
BIOINFORMATICS SIMPLIFIED
BIOINFORMATICS SIMPLIFIED
Platform
Dashboard Home Provides Platform Usage and Resource Consumption Details
RNA-seq data analysis standardization
BIOINFORMATICS SIMPLIFIED
Navigation Menus • Dashboard Menu – Access all platform features • Project Menu – Navigates within a project
BIOINFORMATICS SIMPLIFIED
Multiple Datatypes Can be Uploaded • Sequencing raw data, references, annotation and additional files are uploaded and stored separately
BIOINFORMATICS SIMPLIFIED
Projects Centric Analysis Setup • Projects are mini workspaces that segregate sample sets, pipelines, jobs, and reports • Allows for several sample subsets and multiple executions
Sample Set(s) My Pipeline(s) Job(s) Report(s)
BIOINFORMATICS SIMPLIFIED
Pipeline Library • Warehouse of all the pipelines • Pipelines are grouped into hubs • Copy the pipelines from the library into to a project
BIOINFORMATICS SIMPLIFIED
Pipeline Building Process • Tools are the fundamental structures of analysis; Each tool can execute multiple functions via commands • Commands are wired together to build customized genomics data analysis applications
Pipeline
Add Steps
Commands
Tools
Command Builder • Description • Details • Metadata
Edit default pipeline behavior • Predecessor dependency • Input override • Output override • Merging multiple samples
• • • •
Options Inputs Outputs Arguments
BIOINFORMATICS SIMPLIFIED
Pipeline Execution • Pipeline execution starts with initialization • Reference and annotation files are selected automatically • Execution setup is simple and intuitive - provide sample and condition information and CLICK
BIOINFORMATICS SIMPLIFIED
Jobs • Pipeline running status updates are available under jobs • SAMPLE DEEP-DIVE provides sample level notifications • All the intermediate files and commands are available for data provenance
BIOINFORMATICS SIMPLIFIED
Comprehensive Report View
BIOINFORMATICS SIMPLIFIED
Thank You Very Much for Your Interest
Visit Us
www.stanome.com
Contact Us
[email protected]
BIOINFORMATICS SIMPLIFIED