KNIME User Meetup on Life Science in Boston, July 2016

- Swissnex Boston, Cambridge, MA

The next meetup in Boston on July 12 intends to bring together the KNIME Life Science community for an evening of talks and networking.

Shinichiro Wachi, Proteostasis Inc., Natasja Brooijmans, Blueprint Medicines, and Greg Landrum, VP Life Sciences at KNIME, will each be presenting talks on how KNIME Analytics Platform can be used for drug discovery.

The evening will be an ideal opportunity to get to know KNIME and see how the data- and tool-blending capabilities of this modern data analytics platform can enable science.


• 6 PM A life-science focused tour through some of the new features of KNIME 3.2, Greg Landrum, KNIME

• 6.30 PM Workflow Design Patterns for Assay Data Processing Pipelines, by Shinichiro Wachi, Proteostasis Therapeutics, Inc.

• 7 PM Title Using KNIME to derive knowledge from a fully-annotated kinase-focused compound collection, by Natasja Brooijmans, Principal Scientist, Blueprint Medicines

• 7.30 PM Networking, discussion, food and drinks

The Speakers

Shinichiro Wachi, Ph.D., Sr. Software Engineer, Proteostasis Therapeutics, Inc.

Talk: Workflow Design Patterns for Assay Data Processing Pipelines

Description: A software developer at a small biotech company faces many challenges: limited budget and personnel, ever-changing assays, and demand for rapid turnaround. At PTI, we solved these problems by democratization of automated data processing using the Knime platform. The presentation discusses the combined use of 1) waypoint workflow databases, 2) staged data processing classification, 3) web-based application for data input and reports and 4) workflow distribution using Knime Server to address these challenges for users at all levels of computing expertise.

Bio: I have worked as a software developer at Proteostasis Therapeutics, Inc. (PTI) since 2011.  I have a Ph.D. in Biochemistry from University of California, Davis and a B.S. in Molecular Biology from University of California, San Diego. My past work was mainly in the field of Bioinformatics, starting from multiple protein sequence alignment, gene expression profiling, protein interaction network analysis, and ChIP-seq data processing. My past work as a software developer includes data processing software for high-throughput sequencing data, data visualization application for gene regulatory models, protein network visualization platforms, and numerous bioassay data processing applications. My duties at PTI range from the development of data processing applications to managing bioassay databases. I am currently interested in the use of microservices architecture to accelerate the assembly and deployment of analysis pipelines.

Greg Landrum, VP Life Sciences, KNIME

Bio: Greg focuses on finding (and talking about!) new applications of KNIME in the life sciences and ensuring that KNIME Analytics Platform becomes an even more useful tool for people working in the field. 

He is also the primary developer of the open-source cheminformatics toolkit RDKit. Before joining, Greg was the Global Head of Chemical Information Systems at the Novartis Institutes for BioMedical Research.

Natasja Brooijmans, Principal Scientist, Blueprint Medicines

Talk: Using KNIME to derive knowledge from a fully-annotated kinase-focused compound collection

Bio: Natasja Brooijmans has been Principal Scientist in Computational Chemistry and Cheminformatics at Blueprint Medicines since the company was founded in 2011. Prior to Blueprint Medicines she worked at the Novartis Institutes for BioMedical Research in Cambridge and Wyeth Research. In addition to applying traditional structure-based drug design techniques, cheminformatics methods are applied to analyze the fully-annotated compound collection and understand drivers of potency and selectivity.