Michael Richards Email & Phone Number

North County, San Diego, Ca

I spend my time developing and maintaining three enterprise-wide LIMS systems which I architected. The total cumulative run-time of these systems is 28 years, and they handle a significant fraction of three companies scientific data.Recent work:--Full-lifecycle tracking for biologics. Capturing plasmids, plasmid modification, DNA & glycerol stocks, hybridoma picks, Cell Paste, Supernatant, Purified Protein. Hetro-X-mers work too. All barcoded & location tracked. Calculate Protein properties, capture purification process. Biologics/Small molecule Mixtures track perfectly.--Recombinant Antibody design tools & production tracking.--Providing simple, intuitive visualization tools for a complex clinical trial spanning ex-vivo analysis, MRI data, quality of life, a gazillion biomarkers, and a very complex dosing schedule.---Data mining of UniProt to assist customer with target selection, including custom multiple sequence alignment on specific regions of protein family.---Built custom short-read aligner for illumina NextGen sequencing data in fastq format. Aligns tag-based sequence and barcode to tag using quality score to compute alignment probability. It's the fastest, best tool I know of for aligning probes to their target sequence (NOT to the genome). Can completely process a 50Gbyte, 250M cluster fastq file in under an hour, and give an accurate count of the abundance of each probe by barcode.---Continuing to improve data analysis and visualization tools for Multiparametric data sets, including novel scoring algorithms, custom hierarchical agglomerative clustering and dendrogram generation from scoring, heatmap visualization tools, and aggrigation/visualization tools that allow users to mine through layers of data.--Assembled Gene Expression atlas from NCBI GEO data, merging data across HG U133 Plus 2.0 and HG U133B chipsets.--Built exon database containing human and mouse genome to enable intelligent probe and primer design.

Designed and built scientific informatics platform, fulfilling Informatics, DBA and Developer roles:--Scoped, purchased and deployed: Compellent SAN, VMware cluster on vCenter, Red Hat Linux Server, Oracle Database, Windows 2003 server with IIS webserver.--Developed custom web-based chemical registration and tracking system using Oracle, C#, JavaScript, Daylight Daycart, Chemdraw and ChemAxon tools.--Developed HTS data reduction tools, including nonlinear regression to fit dose-response data, leveraging sample-tracking system to automatically associate assay results with tested samples.--Developed data reduction software for a wide variety of biological assays, provided mechanisms for biologists to record assay protocols and associate experimental results with registered chemical compounds.--Developed automated oligonucleotide design tool to produce PCR primers, TaqMan assays and RASL probes from mixed lists of Gene names, Transcript numbers and Affymetrix Probe ID’s. Based on Human Genome build #19 from UCSC, Primer3 for TM optimization, and novel code to find best region for assay in the transcriptome.--Developed novel tools for reducing, visualizing and interpreting Gene Expression High Throughput Screening (GEHTS) data.--Developed novel algorithms for reducing a 96-300 gene --signature to a single assay-specific score.--Normalized Affymetrix .chp files, Next-Gen sequencing data and Fluidigm qPCR data so that it could be interpreted across platforms in the same visualization tool.--Developed novel tools for Hierarchical Agglomerative Clustering of multiple gene signatures based on novel scoring algorithms.--Developed novel visualization tools for dendrogram generation and results depiction.--Managed contract software developers to meet specific research goals within specified timelines and on budget.--Maintained infrastructure documentation, source code control, and data backup.

Designed and implemented a scientific information database which is central to the High Throughput Discovery efforts at Senomyx, encompassing the operations of Optimization Chemistry, High-Throughput Synthesis, Analytical, Compound Services, Compound Storage, Purchasing, Chemical Receiving, High Throughput Screening, Data Reduction and Cell Culture. Over the course of nine years, we have captured a complete record of every high-throughput screening data point ever produced at Senomyx, from over 200 assays, EC50 values down to the raw time/intensity traces output from the instruments. HTS results are tied directly to a record of the entire lifecycle of a chemical compound from the time it enters the building, or is synthesized, until the time it is exhausted. Cell lines are tracked through their entire lifecycle at Senomyx, and are associated with HTS results, so that biologists can associate assay statistics with cell line performance. The database also captures chemical analytical data, such as purity and reaction yield, NMR spectra, optical rotation, melting point, and solubility data. The data system also guides and manages the workflow of chemical synthesis, and integrates HTS screening requests with our compound reformatting department. Chemicals are purchased and tracked through our online purchasing software. Libraries are developed or purchased through our physical property filtering tools. Screening campaigns can be planned, and costs estimated using historical screening data. All of these functions are presented to the user in one coherent suite of web-based applications, giving scientists access to a complete online record of scientific discovery at Senomyx.Manage documentation, source code control, and project organization.Implemented automated data processing and statistical analysis of scientific data.Responsible for a $1M annual budget Lead and manage a small team of highly skilled developers

Designed a web-based system allowing a scientist to pre-screen and filter virtual chemical libraries using CombiChem’s modeling tools and simple physical property filters. (The group I joined disbanded just as I arrived).

A key contributor to a team which designed and developed an enterprise-wide Laboratory Information Management System (LIMS).Wrote core business-layer COM components, developed fundamental applications.Provided interface definition guidelines, coding standards and guidance to other programmers.Served as network administrator, managed network consultants.

Lead the development of complex, custom laboratory automation systems and software.Specified customers project requirements and managed customer expectations.Produced instruction manuals and complete documentation for all custom systems.Routinely met commitments and timelines and delivered projects on schedule.Developed software/hardware interfaces to a wide range of laboratory devices.Designed and built highly complex multi-processor, multi-process laboratory automation systems.Designed, Developed and Delivered automated systems to: Astra-Draco, Lund, Sweden; NuPharm, Toronto, Canada; Bristol-Myers Squibb, Buffalo,NY; Schering-Plough, Springfield, NJ; 3D Pharmaceuticals, St.Paul, MN; and Chiron Corporation in Emeryville, CA

Initiated, designed, and built prototype processing equipment to explore a range of process variables.Installed and demonstrated equipment feasibility on a prototype production line.