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A two-day hackathon will be held in cyberspace. The event will start at 0700 US Pacific Time Thursday 24th and go for 48 hours ending at 0700 US Pacific time on Saturday 25th of April, 2020. This will allow people to attend from various parts of the globe and join as they are able.
People will hack on data standards to transfer HLA and KIR data, and create code to transfer, transform, annotate and report this data.
This hackathon will focus on three topics:
- The development of a database of HLA and COVID-19 data to support global efforts in this area HLACOVID19.org
- The development of database tools for the [18th IHIW] (http://www.ihiw18.org)
- The development of tools for validating and processing HLA genotyping results in [HML 1.0.1] (http://schemas.nmdp.org) format
There have been nine previous DaSH events across America and Europe.
Further details: Please contact Michael Wright, mwright@nmdp.org or Martin Maiers mmaiers@nmdp.org.
A two-day hackathon will be held on the campus at the University of Colorado, the last Thursday and Friday in May 2019. People will hack on data standards to transfer HLA and KIR data, and create code to transfer, transform, annotate and report this data. As it is a hackathon, everyone is welcome to come and work on their own topic in a room of like-minded people. There have been eight previous DaSH events across America and Europe. For further details, please contact Michael Wright, mwright@nmdp.org or Martin Maiers mmaiers@nmdp.org.
During previous DaSH events, participants helped finalize specifications for MIRING, worked on tools implementing it (e.g., HML 1.0), and considered ways how to express novel polymorphisms without human curation (e.g., Gene Feature Enumeration). Suggested topics for this event include
- Development of Gene Feature Enumeration (GFE) tools to:
- allow dissection of allele names for HLA and KIR
- allow batch conversion of allele names data to GFE
- Updating the GL Service to incorporate UIDs into URIs
- Development of PHYCuS (Public Haplotype frequencY Curation Service)
- HL7-FHIR to report consensus sequence
- Develop a general purpose HLA validation and resolution assessment service
The meeting starts at 8:00 am on Thursday May 30th, finishing about 5:30pm on Friday May 31st 2019. We may extended into Saturday or go hike in the mountains or both.
On the campus of the University of Colorado, Denver. Further details: Please contact Michael Wright, mwright@nmdp.org or Martin Maiers mmaiers@nmdp.org.
During previous DaSH events, participants helped finalize specifications for MIRING, worked on tools implementing it (e.g., HML 1.0), and considered ways how to express novel polymorphisms without human curation (e.g., Gene Feature Enumeration). Suggested topics for this event include
- Development of Gene Feature Enumeration (GFE) tools to:
- allow dissection of allele names for HLA and KIR
- allow batch conversion of allele names data to GFE
- Updating the GL Service to incorporate UIDs into URIs
- Development of PHYCuS (Public Haplotype frequencY Curation Service)
- HL7-FHIR to report consensus sequence
- Develop a general purpose HLA validation and resolution assessment service
The meeting starts at 8:00 am on Saturday 6th, finishing about 3:30pm on Sunday 7th October 2018. This event takes place after the 44th Annual Meeting of ASHI is held in Baltimore. Book your travel accordingly.
On the campus of the University of Maryland, Baltimore. Further details: Please contact Michael Wright, mwright@nmdp.org or Martin Maiers mmaiers@nmdp.org.
We are holding a 1-day educational symposium with topics like:
- Introduction to FHIR
- Resources & Profiles
- Creating and POSTing resource instances: Bundle, Patient, Specimen, Observation, Sequence
- Implementation Guides
- Genomics Reporting Implementation Guide
- Reporting HLA genotyping using the CG IG.
This 2-day Hackathon will be focused on HLA & FHIR. The goal would be to vet the Clinical Genomics implementation guide, specifically for HLA reporting. This will tie in with the Publishing timeline, where the CG workgroup votes on content for the September ballot on August 13th. Additional things to do or work on:
- Cytogenetics
- Registry Use Cases (cross walk EMDIS data dictionary and semantics with HL7-FHIR)
- Hands-on exercises
- Go explore! Both events will take place in the NMDP offices in Minneapolis.
Please contact Martin Maiers for more information: mmaiers@nmdp.org
To focus activity at this event we have produced a list of topics, and will form teams around some of them, depending on what people want to work on. Each team should produce code collaboratively and have a functional demo at the end of the event.
- Modeling peptide processing and presentation pathways (NetChop/Chipper, NetMHC), NeoAntigen Prediction, Whole Genome Sequence Analysis
- HL7-FHIR (HML==> FHIR bundles), FHIR Clinical Genomics, Sync for Genes
- IHIWS follow up (GFE, ACT, KIR, Whole Gene HLA and KIR Analysis)
- Analysis of Primate MHC data using 17th IHIWS Informatics tools
- Haplotype Frequency Curation
Progress Report: DaSH 2017 Progress Report
As usual, there will be an informal meal the evening before the meeting. We will eat at De Zwarte Vosch (http://www.dezwartevosch.nl/) on Sunday 12th November. The meeting will take place at ‘In de Ruimte’ (http://www.inderuimte.org/), on Oudegracht 230, Utrecht. As usual, it will be two days of working, Monday 13th and Tuesday 14th, with lunch and dinner provided. The meeting closes at 4pm on Tuesday, with a dinner for those people staying on. This meeting is timed to allow people to move directly to the HL7-FHIR developer days, taking place in Amsterdam, November 15th to 17th. Please contact Michael Wright for more information: mwright@nmdp.org
You are invited to participate in a data standards hackathon which will take place during the 17th workshop in the “Fred Farr Forum” room. Thursday, Friday and Saturday Sept 7th-9th 9am-9pm
- Whole Gene HLA and KIR Analysis. Automated annotation Gene Feature Enumeration.
- HL7-FHIR: Exchanging HLA and KIR NGS results using Health Level 7 Fast Healthcare Interoperability Resources (FHIR) for Clinical Genomics
- Tools for Allele and Haplotype Frequency Analysis of HLA and KIR
All attendees need to be registered for the IHIWS, but no further registration is required. Further details: Please contact Martin Maiers, mmaiers@nmdp.org
https://bethematch.webex.com/bethematch/j.php?MTID=ma45b422f9c67b4a9727260aa883a67f7
Six Data Standards Hackathons (DaSH events) have been held since Fall 2014. These events are designed for groups of interested people to come together and produce open source software (hack) or decisions that will facilitate the analysis and interchange of HLA and KIR data.
- Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing Human Immmunology, doi:10.1016/j.humimm.2015.09.011
- Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-based HLA and KIR Genotyping, Human Immmunology, doi:10.1016/j.humimm.2015.08.001
- A gene feature enumeration approach for describing HLA allele polymorphism Human Immunology, doi:10.1016/j.humimm.2015.09.016
- https://github.com/nmdp-bioinformatics/dash/wiki
In order to focus the activity at this event we have developed a list of “scrum-team” topics with tangible goals. We will form teams around some of these topics. The team should plan to produce code collaboratively and have a functional demo at the end of the event.
-
Prepare “feature service” for production use • Implement a versioning system for the feature service • Add authentication and security layers • Add curation capability linking sequences to o IPD-KIR and IMGT/HLA Database accession release version and Accession number (a more accurate way of saying the allele name) o the sequence submitter and their “de-novo” identifiers for sequences they have submitted, associated with a given GFE notation/set of locus/feature/rank/accession coordinates • Populate feature service with all versions of HLA.xml and KIR.dat • Improve documentation; make sure that the documentation is sufficient to inform an API for analytics; expand on the BTOP-like pairwise difference annotation
-
GFE service enhancements • Experiment with AWS configurations • Add a database cache • Volume test • Test installation process • Add clients and tools • Rename (service-gfe-submission -> service-gfe) • Connect to feature service with authentication
-
GFE Service validation • Validation of alignments using “features” from HLA.xml and KIR.dat files • Develop automated tests; possibly using Neo4j
-
Improve current capabilities of the annotation pipeline (within GFE service) • Make it a maven project; push code to maven central • Allow GFE service to utilize different version of annotation • Add capability of running ABO
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Haplotype Frequency Curation Service (HFCu) development • Build the shell of the backend based on the population service and check the code into GitHub
In order to focus the activity at this event we have developed a list of “scrum-team” topics with tangible goals. We will form teams around some of these topics. The team should plan to produce code collaboratively and have a functional demo at the end of the event.
- Prepare “feature service” for production use Implement a versioning system for the feature service Add authentication and security layers Add curation capability linking sequences to
- IPD-KIR and IMGT/HLA Database accession release version and Accession number (a more accurate way of saying the allele name)
- the sequence submitter and their “de-novo” identifiers for sequences they have submitted, associated with a given GFE notation/set of locus/feature/rank/accession coordinates Populate feature service with all versions of HLA.xml and KIR.dat Improve documentation; make sure that the documentation is sufficient to inform an API for analytics; expand on the BTOP-like pairwise difference annotation
- GFE Service Enhancements
- Experiment with AWS configurations Add a database cache
- Volume test
- Test installation process
- Add clients and tools
- Rename (service-gfe-submission -> service-gfe) Connect to feature service with authentication
- GFE Service Validation
- Validation of alignments using “features” from HLA.xml and KIR.dat files
- Develop automated tests; possibly using Neo4j
- Improve current capabilities of the annotation pipeline (within GFE service)
- Make it a maven project; push code to maven central
- Allow GFE service to utilize different version of annotation
- Add capability of running ABO
- Haplotype Frequency Curation Service (HFCu) development
- Build the shell of the backend based on the population service and check the code into GitHub
- HL7 FHIR Develop use cases: • Vendor perspective (create partially filled FHIR template)
- identify what vendor software can pre-fill
- e.g. sequence info, allele-assignments, sample identification, methodology • Lab perspective
- fill in the rest of the data not available to vendor software • Transplant Center perspective
- patient demographics, from EMR • Registry perspective
- receive, process and verify bundle Identify required resources for use case Map data to resources • From HML
- build bundle
- POST to FHIR server Create client that will search, GET and link resources from FHIR server. Create a client that will access HLA terminology server.
- Integrate Chipper algorithm for predicting proteasome cleavage sites
- Add to peptide prediction pipeline(s) https://github.com/massie/chipper
Since the HL7-FHIR topic involves a good deal of background we are proposing an educational session in a small breakout room (holds 7) with presentations by Bob Milius and Andrew Brown
- Intro to FHIR (Bob)
- ClinFHIR (general client to build FHIR resources and profiles) (Bob)
- Client to build FHIR resources from HML (Andrew)
#History:
Three DaSH events have been held, in Bethesda, La Jolla and Minneapolis.
Gottfried Fischer is hosting the fourth event in Austria.
#What: ##3 primary focus areas
- Feature Service Ecosystem: building up the tools for getting data in/out of this service in preparation for the 17th IHIW <img src="https://cloud.githubusercontent.com/assets/8570385/19779508/07e3a882-9c47-11e6-9e7c-b90f0050a2fd.png" align="right" >
- REST storage and unique ID generation for locus/term/rank/sequence
- Annotation Service: convert consensus to locus/term/rank/sequence
- GFE Service: use feature service to generate 17th IHIW names
- GL Service: strict relative to particular GFE Service instance (GFE-GL)
- Bulk loading of full-gene NGS data: NMDP 80,000 individuals, other
- Public Curation: associate a “user” with a contribution (HML/cons.)
- Private Curation: segregate PHI/PII from genotype data
- Support beyond classical HLA to non-classical HLA and KIR genomics
- Upload to (and download from) SRA
- HL7 FHIR® (Fast Healthcare Interoperability Resources). We will be exploring the use of HL7 FHIR® to exchange HLA typing dating with the EMRs and other healthcare systems. To prepare for this, the following will be provided ahead of the meeting
- FHIR® resource/profile documentation and introductory material
- Examples of how NGS based genotyping data may be represented in FHIR®
- Link to a FHIR® compliant server which we will use to exchange data
- Webinar presenting an introduction to FHIR® and exchanging HLA genotyping data. For some introductory information, see the Proposed Standard for Trial Use 3 (STU3) at http://hl7.org/fhir/2016Sep and the wiki documentation at http://wiki.hl7.org/index.php?title=FHIR
- Global Haplotype Analysis. Curation/Creation/Population services. Quality metrics. Global HF analysis. AFND/Publication. Licensing and data access.
##Other topics:
-
HML adoption
- Dissemination of the tools to the typing community.
- A publically available pipeline for the analysis of NGS data, which can be used as reference for the validation of new alleles or other typing software.
- A tool that allows the generation of HML from current NGS SW vendor reports.
- Long read data: PacBio, Oxford Nanopore.
- Revisit KIR presence/absence and CNV reporting.
- Long term support of services & interaction with societies: EFI/APHIA/ASHI.
-
Non-coding variation such as the HLA-C miRNA
- Mining and reporting known functional variants from outside codons.
- Automated annotation of non-coding features.
The meeting will start with an informal event on Thursday night, November 3rd. We will work from 8:00 am on Friday 4th, finishing at 4:00 pm on Saturday 5th November 2016, stopping when appropriate to eat and drink and socialize.
On the campus of the University of Vienna, Austria.
Please contact Michael Wright, mwright@nmdp.org
As the name 'hackathon' implies, the meeting is geared to 'implementers,' and less so to 'talkers' and 'directors.'
Using consensus data as specified in MIRING and implemented in HML 1.0, focusing on investigating and developing the best ways of enumerating, analyzing, matching and extracting features.
Implementers will spend two days working on the above goal. As the name 'hackathon' implies, the meeting is geared to 'implementers,' and less so to 'talkers' and 'directors.'
Starting with an informal evening get together on Thursday 11th, work will start at 8:00 am on Friday 12th. We will finish about 4:00pm on Saturday 13th February 2016.
The W hotel, at the Foshay, Minneapolis, MN
Gene Feature Enumeration for HLA polymorphism paper by SJ Mack
Contact Michael Wright at mwright@nmdp.org for more information
Our goal is to produce a service that will interpret novel alleles automatically and utilize HML 1.0 to manage novel variations.
HLA is one of the most medically relevant gene systems in humans. While rare variants are important determinants of disease, common polymorphisms - especially prevalent in HLA - are more important for histocompatibility and donor-recipient matching. Can we build data standards and pipelines that accommodate both?
Adapt, enhance, modify, (hack) our pipeline to process IHIWS samples into (i) consensus sequences and HLA nomenclature (ii) HML 1.0 (iii) Enumerated Gene Features (http://biorxiv.org/content/early/2015/02/15/015222) (iv) Variant, variant effects, and functional/clinical annotation Validate the HML, possibly using either or both of these options. (i) Check/hack existing validation code produced by NMDP. (ii) Consume HML from the above processing, and check that everyone ends up with the same result.
Implementers will spend two days working on new ways to report and exchange HLA and KIR NGS data. We will concentrate on sorting out how to deal with novel polymorphisms. As the name 'hackathon' implies, the meeting is geared to 'implementers,' and less so to 'talkers' and 'directors.'
Data Standards Hackathon - developing a new way to exchange NGS data for HLA and KIR
September 26 & 27, 2014 The hackathon occurred immediately following the FDA Public Workshop: Next-Generation Sequencing Standards. The FDA workshop was focused on next-generation sequencing (NGS) technology, data formats standardization and promotion of interoperability protocols.
The goal of the hackathon was to:
- have implementers work to integrate a toolset with the various NGS systems and analysis software packages currently in use.
Hackathon attendees should be prepared to provide feedback on:
- how well the tools work together,
- how they work with extant NGS software and standards,
- elements that need fixing (and fix them),
- additional elements required to qualify as a MIBBI.
The hackathon’s success was measured by our ability to achieve interoperability for the community and a vetted MIRING and HML 1.0.
Get started with the pipeline tutorial here.