Jeremy Chambers, M.Sc. SE

BIG DATA, Life Science

Application Architect

 

Linked In: http://www.linkedin.com/in/jeremychambers

Email: jchambers@alumni.cmu.edu

 

 

QUALIFICATION SUMMARY:

·         Focus in Life Science, BIG DATA.  Combine experience from Roche 454 Life Sciences and IBM Platform Computing (HPC middleware) to solving Big Data challenges in Life Science.   

·         Thought Leadership.  Analyze and explain relevant trends, generate goals, strategies. Author whitepapers. Define and communicate high level reference architectures, translate into design and test documents.

·         Technical presentation skills and collaboration. Regular speaker at BioIT World. International solution sales to conference audiences, CIOs, Principal Scientists, Architecture teams.

·         Analytics Oriented.  15 years developing high performance analytic engines for start-ups, research labs, and major multinational corporations.  Data Mining /

·         Agile, performance driven.  13 of 25 years in Silicon Valley / SF Bay developing solutions in Java/C++/SOA.  M.Sc. of Software Engineering from Carnegie Mellon University.

 

DOMAIN EXPERIENCE (25 YEARS):

DNA Sequencing, Life Science, Bioinformatics, Health Care, Analytics, Machine Learning, Data Mining, Distributed Computing, HPC, Cloud Computing, Clusters, Energy T&D, Financial Engineering, Signal Processing, Simulation, Government and Corporate sponsored research in context aware multi-modal analytics.

 

BUSINESS SKILLS:

Open collaborative leadership style in cross-functional teams. Collaboratively define, commit to and track progress along continuously optimized delivery trajectories. Identify and manage risk aggressively yet diplomatically.  Contribute to and stimulate team's innovative spark in R&D, look for glide paths to bring the intangible to earth, implement what gets the job done. 

 

 

EDUCATION:

 

Carnegie Mellon University, MS SE (Master of Science in Software Engineering)

§         Agile and Disciplined Methodologies, Architectures, Metrics, Predictable Performance

§         Practicum project: adding rule-engine and sub-symbolic learners to laboratory notebook system

§         CMU Research at Panasonic R&D lab: multi-agent systems in smart consumer electronics

§         Taught SOA / web-services practicum to Lockheed graduate students at NASA campus

§         Wireless agents and video relay using NASA robot and Java + IEEE JADE agents

 

University of Arizona, studied Computer Engineering, Japanese. 

§         Developed robotics and image processing software for world's first 'lensless' microscope

§         NIH sponsored research under CMU prof. Kendal Preston, Jr.: telepathology, digital pathology tools

o        Involved collaboration with IntelliPath (Bayesian based system)

§         Undergraduate research in Japan prototyping VR / augmented reality system for steel pipe repair robot

 

SOFTWARE ENGINEERING SKILLS MATRIX:

 

Bioinformatics	NGS, Bioinformatics, Mapping/Assembly, Resequencing, Amplicon Variant Analysis, SAM/BAM, FASTA, ClustalW, ACE, BLAST, Broad Institute's open source: Picard, GATK. Contrail (de novo assembly).  Metagenomics (BioPig), AutoDock.
MapReduce/Hadoop	Hadoop, IBM Platform Symphony, Contrail (de Novo Assembly), PIG, HDFS
Lifecycle	Agile, XP, SCRUM or hybrid process tailored to your project
Architecture	Hybrid Cloud, Clusters, Distributed, Multi-tier, SOA, P2P/Sockets, Client/Server, Pipes & Filters, OOA/D, Design Patterns. IBM Platform Symphony, IBM Platform LSF (batch oriented scheduling engine).  Amazon EC2, Hadoop / MapReduce, Google Compute Engine (early access)
Languages	Java/J2EE, C++, SQL, UML, XML/XSLT. Familiar with Python and R, PIG and HIVE
IDE	Eclipse IDE, Wingware Python IDE
Continuous Integration	Hudson/Jenkins, Nexus, Maven, Sonar, JUnit, TestNG, GIT, Subversion, familiar with CloudBees, Atlassian onDemand
Threads and Concurrency	java.util.concurrent (Executor) and Java Threads, MPI, Posix/C++, IPC, DSS/CCR (MSRT)
Embedded Systems	Boeckeler Controllers, Intelligent Instrumentation Inc DAQ boards, GAPP II (Geometric Arithmetic Parallel Processor), familiar with MIT Crickets, ARM, GPGPU.
Robotics and RT Middleware	Real time data acquisition, sensor fusion, CMU PER (Personal Exploration Rover), Willow Garage, OpenCV / ROS, kinematics
Artificial Intelligence	Intelligent Agents, sub-symbolic learners and non-linear prediction (neural networks), boosting, symbolic reasoning (rule-engines / declarative programming), collaborative filters, WEKA. Familiar with Mahout, KNIME.
Database and Data-mining	NoSQL, HBASE, Oracle, MySQL, JDBC, SQL, WEKA (machine learners / classifiers), familiar with Splunk.
Computer Vision	OpenCV, pittpatt face tracking and recognition (Pittsburgh Pattern Recognition -- acquired by Google), Google ZXING (QR Codes)
Messaging Middleware	JMS (queues, topics, publish and subscribe), Log4J (logger, socket appenders)
SOA / Web Applications	IBM Platform Symphony SOA services (ultra low latency and parallel compute), Web Services, Apache Tomcat, JBOSS, Servlets
Computational Tools and APIs	Mathematica, MathCAD.  Some tinkering with R, MATLAB
Multi-Agent Systems	IEEE FIPA JADE, P2P Agents, Sockets, client and server-side development, distributed systems
Multimedia/ Visualization	2D and 3D Vector Graphics, Java 3D, OpenGL, Photoshop, Visio, Google SketchUp
Information Security	NIST approved encryption standards
OS	Windows, Linux (RHEL, CentOS, Ubuntu, Fedora), Oracle VM Virtual Box

EXPERIENCE:

 

IBM Platform Computing, Cambridge, MA

July 2011 - Present

Initially at 'Platform Computing', acquired by IBM.  Solution Architect at intersection of Life Science + BIG DATA + HPC.  Evangelize value of low-latency grid-middleware and hybrid-clouds for both data and compute intensive workloads to Life Science community (primarily). Support solution-sales in cross functional teams by explaining superiority of Platform's MapReduce accelerator over open-source Hadoop.  Analyze and respond to complex bid for tender and RFPs (including a win of a ESA's GAIA Space Telescope in UK).  Devise and lead complex collaborative POCs and comparative benchmark R&D. Participate in opensource (Cold Spring Harbor Lab's Contrail) and other architecture reviews (Broad's GATK).  Author 'thought leadership' whitepapers, webinars, and slide presentations.  Prepare and deliver talks globally including at BioIT World events, client sites, IBM R&D sites, and various US Federal and foreign agencies.

 

454 Life Sciences, A Roche Company, Branford, CT

April 2009 - April 2011

Architect / Sr. Software Engineer.  Consulted on machine-learning POCs using WEKA (N Fold Cross Validation, Naive Bayes, J48, Neural Nets), i.e., classification of pairwise sequence overlaps through machine-learning inferred biological significance.  Took over development of Java based software (GS Amplicon Variant Analyzer) for use on Roche NGS platforms (i.e., Genome Sequencer FLX, GS Junior System). Lead architectural reverse-engineering and code-refactoring. Assisted other developers with various image processing and bioinformatics library testing.  Wrote Java components to translate Roche proprietary nucleotide data-model into ACE, CLUSTAL, FASTA, TSV/CSV, SAM/BAM formats for interoperability with 3rd party tools and systems. Audited, debugged and maintained continuous-integration POM files and jar repository (Maven 3.x, Nexus, Hudson/Jenkins) which also automated tracking of various quality metrics (Sonar). Co-developed high-speed nucleotide-(de)compression algorithms. Utilized YourKit to benchmark and optimize. Built TestNG/JUnit based test-center for large genomic data validation. Evaluated various 3rd party tools such as Picard API, IGV, Galaxy, HapMap. Participated in complex bug triage and data science investigations.

Appscio, Silicon Valley

March 2008 - December 2008

Consulting Sr. Software Engineer (via XcelAgent, above). Metadata harvesting from within media to enable indexing and segmentation. Pipeline enabled composability of plug-in features such as transcoding and analysis-tools that utilize face-finding, Speech to Text (STT), Speaker Diarization, Video-OCR.  Collaboratively refined architecture, detailed design and test plans. Conducted C/C++ framework integration/characterization R&D. Collaboratively tailored agile infrastructure and processes to maximize quality and speed of delivery. Conducted system performance-characterization. Participated in the Technical Advisory Board, peer-reviewed the work of other teammates. Delivered first Beta product on time to first US customer. Evangelized open-source vision in Tokyo to Program Director of Next Generation Robots in CSTP.  

 

Carnegie Mellon University, Silicon Valley Campus

October 2007 – March 2008

Research Consultant (via XcelAgent, above).  SAP sponsored R&D for context-aware vision system: developed proofs of concept using Haar based face-recognition and Google's open source vision based QR-code reader.  Also studied Kalman filter based sensor-fusion for location-estimation. “Instrumental in exceeding sponsor's expectations”, delivered early and under budget.

 

XcelAgent Software Consulting, Silicon Valley & New England

July 2000 - Present

Principal, Consultant.  Custom Java/C++/AI distributed software to sense, analyze, learn, reason, act. Example clients include: Alstom, Appscio, Areva, Carnegie Mellon University, Lockheed, SAP R&D (at CMU).

 

 

Additional Selected Experience Summary (1988 - 2007):

·         Kensal Corporation – tele-pathology software, lensless microscopy, image processing. C/C++, ASM

·         Hitachi - clinical treatment pathway analysis software, data mining, HL7.  C/C++, Java

·         Alstom – hydro-electric dam, energy accounting system. Java, C++/STL, Mathematica, Oracle

·         Nippon Steel – augmented reality R&D for steel pipe repair robot under University of Tokyo team lead

1	More about Jeremy found here: http://www.linkedin.com/in/jeremychambers