SOULCAP is Go! SOULCAP (Standardized Ontology Unique Labelling for Cytometry Annotation of Populations, a working title for now - so named for largely sentimental reasons) project has started for real. This aim is to deliver a free, open, public, community resource and reference software tools to standardize cell population names identified by cytometry, no matter what the analytical approach (manual gating, dimensionality reduction, clustering), and link these to ontologies. Right now efforts are focused on organizing the effort into five working groups, and linking to the major flow societies to make sure this is done right for benefit of all. If you be interested in any of working groups below let me know. If you have already you should have got an email yesterday. There is no barrier to entry other than interest and willingness to contribute. One hope is by crowdsourcing a lot of the effort there is low expectation to your time commitment. 1) Project management. 2) Bioinformatics - Develop the software and data standard that will glue this project together. Provide a reference implementation thereof. Figure out how to connect this to all the dimensionality reduction and clustering methods so everything (in the background) uses the same computational ID. How do we align ungated data with the reference map? Lots of other fun puzzles here to solve. 3) Label/Annotation - Decide which section in a gated plot gets anointed with the label T-cell from now and ever more, to be used by everyone. Plus all the other canonical cell types. Easiest job ;) These labels will be then tied to the computational IDs. My $.02: peer reviewed literature should back up every assignment. 4) Ontology - Figure out how to tie the computational IDs to the Cell Ontology (and hopefully vice versa), along with other ontologies. This will make magic happen. Super excited to see this happen! 5) Outreach (aka Adoption, AKA Enablement, AKA Knowledge distribution). Work with stakeholders such as software houses and societies (e.g, there is already a call scheduled this week with leadership of all the major flow cytometry societies) to make sure what we are doing will make everyone who is not part of this effort and who uses cytometry will be happy and do better, bigger science, faster.
About us
No one knows your data like you do. That's why we use the knowledge you've built into your gating hierarchies to customize bioinformatics pipelines that can analyze your flow cytometry data better and faster (a couple of seconds per file) than you would have by manual analysis. Our workflows leverage algorithms we developed in-house, and that have consistently been peer-reviewed to be the best performing and state-of-the art. We also have experience with all the commonly used automated tools for the automated analysis of flow cytometry and mass cytometry (CyTOF) datasets. We have applied our analysis approaches on research and clinical trial data covering the spectrum of immunology (ALS, HIV, HSV vaccines, various cancers (including leukemia and lymphoma, prostrate, oral), TB, GvHD, solid organ transplantation, atherosclerosis, cancer immunotherapy, influenza) so you can rest assured you are covered. Cytapex Bioinformatics Inc. removes the barriers to high throughput / high dimensional cytometry data by providing expert services in data management, quality checking and data analysis including customized gating and biomarker discovery pipelines. Our client list includes basic researchers, clinicians, testing service providers, small and big pharma and clinical trial groups.
- Website
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http://cytapex.com
External link for Cytapex Bioinformatics Inc.
- Industry
- Research Services
- Company size
- 2-10 employees
- Headquarters
- Burnaby, British Columbia
- Type
- Privately Held
- Specialties
- flow cytometry, bioinformatics, ddPCR, CyTOF, data analysis, and Mass cytometry
Locations
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Primary
Get directions
9330 Univeristy Crescent
#200
Burnaby, British Columbia V5A 4X9, CA