Experience — Philippe Soares

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Experiences

Was the architect and tech lead for a cloud based cancer diagnostics solution.
Lead a team of 13 developers.
Trained the teams on all the backend technologies of the stack:
- Ontologies: concepts, data formats, storage and management with triple stores, sparql, federated queries.
- Asynchronous services using Reactive Java (Project Reactor) and Apache Kafka
- Java microservices using Spring, then Micronaut.
- Containers: usage, building, securing and optimizing, using Docker.
- Kubernetes: creating artifacts using Helm (deployments, jobs, cronjobs, secrets, persistent volumes, etc.).
- Monitoring containers using Grafana and Prometheus.
- Managing data using MinIO and Amazon S3.
- Optimizing data pipelines using the S3 SQL API.
- Creating a service mesh with Istio (container networking, authentication, ingress and egress gateways).
- Monitoring the service mesh using Kiali.
- Creating and deploying serverless functions in Kubernetes, using OpenFaaS.
- Coordinating asynchronous serverless functions through messaging.
- Linux shell scripting.
Implemented a FHIR compliant response adapter enabling the translation of domain concepts to FHIR responses of any version (Patients, Diagnostic Reports, Diagnostic Requests, etc.).

Was the lead architect for LifeQuest, a search engine that allows patent searchers and scientists to perform full text searches on over 15 million patents in the biological space, with the help of biological ontologies.
Deployed a staging environment for LifeQuest on a docker swarm cluster.
Created a web application for LifeQuest's real-time usage monitoring, using spring integration, meteorjs, graphite, statsd, grafana, mongodb.
Created continuous integration builds for LifeQuest using Jenkins 2 and the docker pipeline plugin.
Created environment developments for GenomeQuest and LifeQuest, using docker compose.
Trained a team of 3 developers on Java and related technologies. In particular to the Spring framework and related sub-projects Spring batch, Spring integration and Spring data.
Currently leading the team to refactor GenomeQuest and LifeQuest's data acquisition pipelines into a unified process, using the technologies above.

Participated in the development of GqDx, a tool for helping researchers diagnose inherited genetic diseases. In particular, created the web based user interface, helped defining backend APIs to manipulate SNP information in hgvs format. See http://www.bio-itworld.com/2011/06/21/university-iowa-develops-genetic-diagnostic-test-hearing-loss.html.
Created the first external cloud version of the company's flagship product, GenomeQuest, on Amazon AWS.
Participated in the development and maintenance of customer workflows.
Environment: linux, php/mysql, javascript (dojo toolkit).

Performed level 2 support of JEE applications for enrollment of patients in clinical trials, patients randomization and electronic data capture.
Developed a time tracking application for the support team, using grails and the ZK framework (in particular ZK calendar).
Environment : java, grails, spring framework, Oracle.

Project leader for bioinformatics : Integrated scientific applications through data federation engines (SRS - Biowisdom), K3 (IDBS) and KDE (Inforsense).
Project leader for the Research IT Business Intelligence : Business Objects XI + Oracle Datawarehouses.
Project leader for Collaborative Software : eRoom (Documentum) and MOSS 2007 (Microsoft).

Project manager, with a team of 3 developers in bioinformatics and molecular modeling projects.
Participated in the setup of a virtual screening facility consisting of a linux cluster of 100 CPUs (50 nodes).
Integrated various software as workflow components into pipeline pilot and InforSense KDE.
Unified bioinformatics content updates using GetDB (Genomining).
Created virtual screening pipelines using pipeline pilot and third party molecular docking software (FlexX, Surflex, GOLD).
Created scientific workflows for several "omics" platforms (microarrays, qPCR, proteomics), using workflow tools : pipeline pilot, InforSense KDE (and a few prototypes with Knime).
Environment : linux, oracle, java, perl, pipeline pilot, inforsense KDE.

In charge of setting up, managing and keeping the bioinformatics platform up to date.
Created a workflow for identifying novel GPCRs, using perl and the sequence comparison engine Biofacet (aka LASSAP).
Maintained genomic and protein sequence databases in various formats (flat files and Oracle databases).
Environment : linux, oracle, perl.

Worked on mediation software, in several teams affected to different worldwide customer accounts.
Software development (ANSI C on various UNIX OSs)
On-site support and consultancy on various worldwide customer locations (El Salvador, Netherlands, Portugal)

Philippe Soares