Project Manager Engineer

Jonathan Chen

*** *. ****** **. #*, Orange, CA 92868

******@***.***

www.ics.uci.edu/~chenjh

626-***-**** (cell / voicemail)

Education

University of California, Irvine Fall 2002 Present

Medical Scientist Training Program (MD/PhD)

School of Information & Computer Science

Basic Sciences Certificate of Excellence (2002-2003)

US Medical Licensing Exam (USMLE) Step 1: 255 (2004)

Educational Affairs Service Award (2004-2005) for self-initiated design

and development of an assignments and scheduling system for medical

student cooperative learning and elective scheduling programs

Bioinformatics Training Grant (NIH) (2005-2006)

ARCS Foundation Scholarship (2005-2006)

University of California, Los Angeles Fall 1996 Winter 2000

B.S. Cybernetics with Specialization in Computer Studies

GPA: 3.90

Medical College Admissions Test 1998: 13/14/13 (99th percentile)

College Honors, Departmental Honors, Summa Cum Laude

Dean s List (1997-1998)

California State University of Los Angeles Fall 1994 Summer 1996

GPA: 3.74

Dean s List (1994-1995, 1995-1996)

Honor s Student of the Year, Nominated (1994-1995)

Selected into Early Entrance Program: Began full-time college attendance

at age 13

Research Experience

UC Irvine, Dept. of Computer Science, Baldi Lab Summer 2004 Present

Developed toolkits to process chemical database.

Made web available interface for searching and processing.

Developed kernel methods based on SMILES strings and 3D structure

Analysis, including clustering of predicted vs. experimental 3D structures

Presentation of process and results at 2005 UCI MSTP Retreat, various

poster symposiums

UC Irvine, Dept. of Computer Science, Lathrop Summer 2003

Integrate tool sources to produce surface data

Geometric transformations and projections into flattened surface

Application of useful descriptive data (electrostatics)

Linear interpolation technique to enable valuable "diff" surfaces

Feed of surface data into machine learning algorithms

Correlation of results against other analysis (3D position)

Presentation of process and results at 2004 UCI MSTP Retreat

UCLA Brain Research Institute, Schlag LabSummer 1998 Spring 1999

Research Student

Developed an automated and more precise data analysis method using

Excel macros (VB for apps)

Teaching Experience

UC Irvine, School of Medicine 2004 2005

Medical student tutor

Anatomy, Immunology, Neuroscience

Kumon Math Center Summer 1995

Tutor

Work Experience

20th Century Fox, Information Tech. Summer 2001 Summer 2002

Software Developer, "Tuscany/Provence" Accounts Receivable, Contract

Maintenance Application

MVC Architectured multi-tiered application. JSP, Servlet web-tier, Session

EJB business tier, JDBC, Oracle database.

Single-handedly championed effort to introduce automated testing and

quality process, beginning with PowerPoint presentation to department IT

group.

Implemented first framework for automated application testing: unit testing

(JUnit), functional testing (Astra QuickTest), the results of which the

project manager declared invaluably paid for itself 3-fold.

JUnit testing framework developed included mock object representations

of HttpServletRequests enabling testing of servlet APIs.

Pushed initiative to employ issue-tracking tool as part of quality process

plan to facilitate management and communication among the team,

including a user accessible version as a medium for users to direct

requests and bug reports directly to team.

Ideas sparked force behind design of sophisticated user security model,

which accounts for both user functional roles and context of secured data.

Crafted elegant, reusable, object-oriented approach to provide powerful

"column-sorting" feature for all application data tables.

Performance tuning employing tools and techniques such as JProbe,

JDBC 2.0 "Batch" statements, assurance of proper table indexing, table

denormalization.

Major contributor to recruiting process of concrete technical skills

assessment questions (e.g. pseudo-coding algorithms during interview)

which greatly increased efficacy in discerning candidates abilities.

Conceived of and implemented many UI and layout enhancements to

improve usability such as for selecting a set of items from a long list of

items. Previous design was list that required "Ctrl+Click" of successive

items. New design separated into "Available" and "Selected" list with

JavaScript enabled buttons to move items between lists. Display of list

item detail on mouse-over. Simple, but highly effective. Manual sorting of

list of objects, JavaScript to enable move up/down, cut and paste features.

Contributed to design of code generator that read Oracle metadata to

generate simple JDBC calls to find and persist Java bean objects as rows

in DB table.

Created JSP prototype of screens for second phase of development.

Tangible enough for users to understand consequences, tradeoffs.

Efficiently produced, "sketch," but convincing enough to be of high value.

Considerably more than "paper & pencil" mock-ups previously used.

Led presentations to key business users of prototype, complicated

functionality such as License Rights management and fee calculations,

taking advantage of detailed knowledge beyond business analyst s level of

detail knowledge. Furthermore, produced development and user

documentation to support presentations.

Identified and resolved several key issues in migration from Weblogic 5.1

to 7.0, where previously constructed unit test suite and automated function

regression tests definitely helped significantly.

Researched and implemented "file upload" feature, from parsing

Multipart/Form-Data encoded Http Requests to streaming binary data into

Weblogic/Oracle JDBC "BLOBs."

Conceived of and implemented framework to easily accept both US and

international date formats (parse as day or month first) by considering

each users request Locale.

Environment: Weblogic 7.0, 5.1, Java, J2EE, EJB, JSP, Servlets, Oracle

8i, JDBC, JavaScript, CSS, JUnit, Astra QuickTest

Trilogy Software Summer 2000 Spring 2001

Software Engineer / Quality Engineer

Developed project quality plans, educated and coordinated teams in

quality processes

Presales Development, Lucent Solutions, Avaya Communication

Produced demo application for Avaya sales cycle, which impressed VP

enough to refer to CIO

Integration Consultant at Williams Communications Solutions

Coordinated team of 10 to update application site for cross-browser (IE

and Netscape) compatibility. Spearheaded the effort and produced HTML-

JSP guideline document for continued development.

Developed reusable HTML-JavaScript calendar widget, plus Java date

forecast validation control.

Prototype Development, Lands End

Created Java-Swing dynamic search tree control for searching an attribute

based item catalog.

Environment: Java, JSP, MS SQL Server, Proprietary "Multi-Channel

Commerce" platform comparable to J2EE

20th Century Fox, Information Tech Summer 1999 Winter 2000

Software Developer, "Atlas" Home Entertainment International Sales Forecasting

Application

Data modeling, design, development and deployment of distributed 3-

tiered applications

Integrated ActiveX spell checking component with existing application

Efficiently solved problem using object metadata (reflection/introspection)

in ways others thought impossible

Integrated complex persistence of data from web-based UI to database in

days when others only made progress in weeks

Environment: Forte (Express), HTML, JavaScript, Oracle 8i

Skills

Category Skill Rating

Development Language Python 3

Java 3

JSP 2

JavaScript 3

HTML, CSS 3

SQL 3

PL/SQL 1

C / C++ 2

Visual Basic 2

Forte (Express) 1

Perl 1

ColdFusion 2

Database System Oracle 8i 2

MS SQL Server 2

MS Access 3

TOAD 2

PostgreSQL 2

Development Tool CVS (WinCVS) 3

Visual Source Safe 1

Perforce 1

JSwat 2

JProbe 1

W indows XP/2000 3

MS-DOS 3

Unix OS 2

Makefile 1

ANT 2

Automated Testing Astra QuickTest 3

Silk 2

W ebload 2

Junit 3

Development Technology J2EE 2

EJB 2

Java Servlets 2

JDBC 2

Swing 1

W eblogic 7.0, 5.1 2

XML 1

TopLINK 1

Java3D 2

VRML 2

Productivity MS Word 3

MS Excel 3

MS PowerPoint 3

Paint Shop Pro 3

Visio 1

DreamWeaver 1

Scientific OEChem 3

Ogham / OEDepict 2

MSMS (Molecular Surface) 2

OpenBabel 1

Corina 1

Selected Presentations

Jonathan H Chen, Peter Phung, Pierre F Baldi. Synthesis Explorer:

Dynamically generated reaction and synthesis problems for organic

chemistry education. ACS National Meeting, Chicago, IL, Spring 2007.

Jonathan H Chen, Erik Linstead, S Joshua Swamidass, Dennis Wang,

Yimeng Dou, Pierre Baldi. ChemDB: A public database of small molecules

and related chemoinformatics resources. ACS National Meeting, Chicago,

IL, Spring 2007.

Jonathan H Chen. Chemical Informatics: Database Searching, Similarity

Measures and Property Prediction. National Library of Medicine Training

Conference, Vanderbilt University, Nashville, TN, Spring 2006.

Publications

Chlo -Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass,

Jonathan Chen, Liva Ralaivola, and Pierre Baldi. One- to Four-

Dimensional Kernels for Small Molecules and Predictive Regression of

Physical, Chemical, and Biological Properties, Journal of Chemical

Informatics and Modeling, (2006) In press.

Jonathan Chen, S. Joshua Swamidass, Yimeng Dou, Jocelyne Bruand,

Pierre Baldi. ChemDB: A Public Database of Small Molecules and

Related Chemoinformatics Resources, Bioinformatics 21: 4133-4139

(2005).

S. Joshua Swamidass, Jonathan Chen, Peter Phung, Jocelyne Bruand,

Liva Ralaivola, and Pierre Baldi. Kernels for Small Molecules and the

Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity. Proceedings

of the 2005 Conference on Intelligent Systems for Molecular Biology,

ISMB 05. Bioinformatics, 21, Supplement 1, i359-368, (2005).

S. A. Danziger, S. J. Swamidass, J. Zeng, L. R. Dearth, Q. Lu, J. H. Chen, J.

Cheng, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, Rainer K. Brachmann, and

Richard H. Lathrop. Functional census of mutation sequence spaces: The

example of p53 cancer rescue mutants. IEEE Transactions on Computational

Biology and Bioinformatics, (2005).

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