Anthony L. Leotta

Software Developer

120 Bayberry Lane

Levittown, NY 11756

Current Technical Skills

C/C++, STL and Boost, Qt, Python 2.x, 3.x, R, PHP, JavaScript, Ruby, Java

Angular JS, jQuery, Adaptive and Responsive Design, Twitter Bootstrap 3

MySQL, PostgreSQL, Oracle, MS SQL Server/Sybase, SQLite

Project Management, Git, Mercurial, Unit Testing

Windows, Linux, HPCC (High Performance Computer Cluster)

Distributed Programming (TCP, Reliable UDP Broadcast), Multithreaded Programming, Distributed

Parallel Computing, Low Latency/High Throughput, Model Driven Design

Experience

Cold Spring Harbor Laboratory

Computational Science Manager III

Cold Spring Harbor, NY

May 5, 2005 - Present

• Completed visualization and data analysis of Next Gen Illumina Sequencing Single Cell Human

Cancer Data for publication

• Created full featured Next Gen Sequencing LIMS for CSHL Illumina and PacBio Sequencing Core

• LIMS = Laboratory Information Management System.

• Supports sample tracking, sample bulk upload, custom clinical parameters.

• Supports GAIIX, HiSeq, MiSeq, NextSeq.

• Supports DNA barcoded multiplexed Illumina libraries. Supports different barcode

protocols including multiple barcode sequences per input library.

• Lab Tech can follow library processing status with email notifications

• Has a role-based permission systems that allows fine grain access control.

• Has a site search that follows associations and relationships between data entities.

• Has a query builder with persistent state which allows users to find things by applying

multiple query filters.

• For more info see poster : http://leotta.com/doku.php?id=limseln:lims

• Documentation : http://wigler.cshl.edu/seqlimswiki/doku.php

• Developed data mining applications that ran on parallel compute clusters using Sun Grid Engine

(SGE)

• Integrated HPCC (High Performance Compute Cluster) pipeline into LIMS. Wrote job manager

that created SGE jobs and updated status of completed jobs in a SQL database.

• Created an ETL (Extract, Transform and Load) library called pyData. Our ETL library accelerated

data handling drudgery by enabling our pipelines to be automated and repeatable, while still

being flexible and adaptable to new schema and business rule changes.

• Analyzed cancer data sets.

• Analyzed whole genome Illumina sequence data.

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(516) 384-3849

tony@leotta.com

• Created custom visualization tools for: tiling arrays for autism and cancer study, trio based

cancer susceptibility analysis, trio/quad based autism study,

• Created desktop visualization tools using Python, R and S-Plus.

• Created web-based visualization tools using JavaScript libraries D3,YUI, jQuery and Raphael.

• Created visualization software in S-Plus that displayed CNV (Copy Number Variants) loci of

interest supporting zoom on event break points, overlay of genes, overlay of raw data, overlay

of different versions segmented data, overlay of various filters (T-cell receptors, immunoglobulin

regions, common polys).

• Created experimental genome browser customized for family-based copy number analysis.

Genome browser supporting multiple individuals, families and any arbitrary sub-set based on a

variety of experimental and clinical parameters to be displayed simultaneously.

• Developed processing pipeline and visualization software for copy number changes in tumors

versus normal adjacent tissue and blood from same individual.

• Created validation software that compares tiling arrays with other array designs in order to

visualize DNA structural variations in individuals, families, tumor versus normal, populations of

affected, populations of normal, etc.

• Built web-based tools:

• Gene Tool - Searches micro-array data for your favorite gene.

• Study Tool - Finds the most frequently amplified or depleted genes

• Gene Info - Access by a list of genes, returns all start and end positions.

• Region Tool - Access a chromosome start and end; finds amplifications or deletions.

• Frequency Tool - Access a chromosome start and end; finds the frequency of all

amplifications or deletions within that region.

• Gene Correlation Tool - Finds the correlation between copy number and expression.

• Created many databases to support the study of human disease. Developed techniques for the

rapid discovery, import, cleansing, normalization, integration, aggregation of “big” data in

excess of 100,000 gig, but also hundreds of thousands of small data files.

• Developed large scale SQL databases (>500 million rows per table) and tuned them to yield subsecond

response.

• Developed ultra-large scale NoSQL databases capable of >2 million inserts per second,

continuously with multi-CPU access using HDF5 in C++ and Python.

• Designed and developed ETL software and created multistage ETL pipelines.

• Simultaneously (sometimes in the same day) used a variety of software packages and tools

including C++, Python, Perl, Linux Bash shell, PHP and R.

• Implemented both SQL and NoSQL solutions.

Publications

• [2013] The Contribution of De-Novo and Rare Inherited Copy Number Changes to Congenital

Heart Disease. Human Genetics

• [2012] De-Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74: 285-299.

• [2012] Reducing System Noise in Copy Number Data Using Principal Components of Self-Self

Hybridizations. Proc. Natl. Acad. Sci., USA, 109: E103-E110.

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• [2012] Rare De Novo Germline Copy-Number Variation in Testicular Cancer. The American

Journal of Human Genetics, 91: 379-383.

• [2011] Inferring Haplotypes of Copy-Number Variations from High-throughput Data with

Uncertainty. Jun;1(1):35-42. doi: 10.1534/g3.111.000174. Epub 2011 Jun 1.

• [2010] Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders

• [2009] Microduplications of 16p11.2 are Associated with Schizophrenia

• [2007] Strong Association of De Novo Copy Number Mutations with Autism

• [2007] A Unified Genetic Theory for Sporadic and Inherited Autism

• [2006] Mouse Genomic Representational Oligonucleotide Microarray Analysis: Detection of

Copy Number Variations in Normal and Tumor Specimens (2006)

NYU/Poly

Adjunct Professor

• Adjunct Professor with Computer Science Department

• Taught graduate level Computer Architecture I and Operating Systems I

Pillar Software, Inc.

Consultant/Software Developer

C# OMS (Order Management System)

• Designed and developed OMS, front-end and back-end.

• Used FIX Server middleware

• Authored real-time multi-threaded front-end that updates GUI.

• Created custom controls on client side to reduce coding.

• Used SQL Server for history, but a faster leaner ISAM database for real-time messages.

Inter-Market Trading System (Wolverine Trading, Equitec, CBOE)

• Developed ITS Trading System in Visual Basic 6.0, C++ and SQL Server 2000

• Used real-time market data from Reuters.

• Connected to CBOE/SIAC system via TCP/IP.

• Supported confirms/cancels for ITS commitments; displayed history of commitments; displayed

running totals of #shares bought/sold, commitments received and commitments canceled.

• Developed C# and VB.NET interfaces for front-end and back-end.

Equity Basket Trading Intelligent Order Execution System (Wolverine Trading, Chicago, IIl)

• Designed and developed Basket Trading/Market Making trading system in C++, SQL Server 2000

and Reuters Market Data.

• Interfaced to multiple ECN’s using FIX protocol.

• GUI features: Products/Indexes, High Speed FIX Message handling, ECN Route Definitions, Order

Profile, Order Entry, Order Status, Real-Time Data Interface, Order History and Order Execution

Detail.

• GUI and all servers were built in C++/SQL Server.

• Built Spear, Leads & Kellogg Trade Activity Reporting System using Borland C++ and SQL

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NY, NY

1999 - 2005

Brooklyn, NY

2013

• Created dozens of web-based reports including: Trade Summary Reporting, Profit & Loss

Reporting, Trade Analysis Reporting and Slippage Reporting.

• Created a stand-alone Clearing Report Generator (uploads to MLCO and SLK) to streamline the

end-of-day processing.

• Created a Web-based Trade/Clearing Problem Tracking System to help manage problems.

• Managed team of developers

Real-Time Call Center System (NAC Marketing, Hicksville, NY)

• Developed complete end-to-end Call Center Application, using MFC C++, VB 6.0, SQL Server

2000 and Low Level PBX Interface.

• Created multi-threaded C++ server with overlapping I/O, completion ports and worker thread

pool that expands and contracts dynamically with work load.

• Real-time payment approval interface in TCP/IP; real-time interface to PBX in TCP/IP.

• Managed team of developers that I hired to help me on this project.

AVON

• www.avon.com

• Designed and coded backend of AVON E-Commerce web site using Solaris, Sybase and C++.

SONY North America

• http://www.sony.com/

• Designed and developed Web site for Sony based on a "data-driven" model. The entire site is

made up of pages that are created "on-the-fly" or during a batch process.

• This allows SONY to change the prices, products, add new products, and remove discontinued

products.

• The dynamic nature of the site is also augmented by a set of "maintenance" screens, that allow

the web master to update the site without any additional programming.

• The site was written in C and C++ using first ISAM database for speed, then the Illustra objectrelational

database.

• Steven Jobs said of the site “This is what a web site should be”.

SONY Music

• http://www.sonymusic.com/

• Developed home page news and artist news for Sony Music.

• HTML was generated from database using C and the Illustra Web data-blade.

• Sony Music divisions, (Columbia, Epic, Classical/Legacy) and the artists enter news items into a

database. The system then generated a series of different web-pages depending on the target

audience. (www.sony.com, Freeloader, etc.) The static pages are generated whenever a news

item is entered.

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Bob Dylan

• http://www.bobdylan.com

• Developed a working prototype of Bob Dylan’s Web site, which Sony Music approved.

Market Vision/Bridge

Consultant/Software Developer

State Street Bank

• Designed and developed back-end server components of FX-Connect Foreign Currency system

using C++ and Sybase on Solaris UNIX. Used FIX protocol.

• Developed global distributed Money Market Trading System Exchange using C++, Microsoft

COM, Sybase and MFC on Windows and UNIX platforms. Used FIX protocol as middleware.

Market Vision

• Designed and developed Open Name Service, a translation server system for mapping one

symbol naming system to another. The translations took Ticker Symbols and converted to CUSIP

or RIQ to CUSIP.

Sybase

Consultant/Database Developer

Teleport

• Installed Sybase Replication Servers in a lab setting to analyze performance and to test various

configurations.

Reuters of America

• Wrote front-end for operations staff in Windows 3.1 using Visual Basic 6.0 and Windows SDK.

Installed and configured Sybase (SQL Server). Wrote programs to reconcile billing and

permission data, using stored procedures, triggers, and SQR.

JP Morgan

• Developed High Availability System for STARS, in a joint project with SUN Microsystems and

Fusion. The HA system monitors critical servers, (i.e. Sybase), network, links and vital resources.

(C, UNIX, Sybase)

Paine Webber

• Designed and developed automatic software installation system (ASIS) for remote installation of

Sybase layered products, application software and utilities.

• Used C, DB-Library, Korn Shell, and Erwin CASE.

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NY, NY/Emeryville CA

1991 - 1994

NY, NY

1994 - 1999

American Express Travel Group

• Created application code for IBM Mainframe interface, SAS Interface, Reporting, Data Loads,

Data Validation, and Version Control System.

• Used C, DB-Library, stored-procedures and SQL Server 4.9.2 under IBM/AIX.

Morgan Stanley

• Played key role in downsizing the Capital International Perspective production from IBM main

frame technology to a SUN/UNIX/Sybase/X Windows environment.

• Extensive use of SQR Reporting language.

Thompson Financial Networks

Financial Developer

NY, NY

1990 - 1991

• Designed and developed distributed applications under UNIX using C, C++, Motif X/Windows

and Sybase. Applications involved the distribution, presentation and analysis of Real-Time and

historical financial data.

• Developed a transaction processing client/server under VAX/VMS and UNIX that communicated

using TCP/IP and DECnet to the UNIX workstations. The server multiplexed workstation requests

to a limited number of Sybase DB-Library connections. Used BSD Sockets and TLI.

• Wrote UNIX workstation applications using Motif and socket interface to gain access to the

transaction-processing server on the VAX. Both the standard Motif library API calls and UIL code

was used to create complex data entry forms, scrolling text boxes, context sensitive help

system, pop-up/pull-down menus, dialog boxes, etc.

• Wrote "Norton Desktop" like program for UNIX, to perform disk, file, and data maintenance

operations. The program was written in Motif and X-Lib.

Spectrum Communications

Programmer

Hicksville, NY

1989 - 1990

• Developed software in C and Assembler for real time 68020 based telecommunications, radio

paging and voice mail system. Developed custom communications protocols, language parsers,

debugged SCSI device drivers, wrote X.25 PAD interfaces, debugged and modified Async and

Ethernet device drivers. Maintained and production built process under DCL and custom version

control software.

• Wrote international paging feature that allowed customers to travel around Europe and still

receive their pages via X.25 communication between paging systems. The system used an Oracle

Database on a VAX/VMS system that communicated to the main SCE paging system via custom

protocols. Customers accessed the feature through a touch-tone keypad interface, which

provided a multi-lingual sampled voice instruction.

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Bell Aerospace Textron

Field Engineer

Wheatfield, NY/Cape Canaveral, FL

1985 - 1988

• Held Secret Security Clearance.

• Was as part of "at Sea" test program aboard USNS Vanguard supporting the GSS (Gravity Sensor

System) of the Trident II project for the U.S. Navy. GSS is part of the navigational sub-system of

the Trident II nuclear submarine, that corrects the inertial navigation system for gravity

anomalies due to geographic features of the ocean floor.

• Liaison between US. Navy, UNISYS, Department of Defense, and Bell Aerospace.

• VAX/VMS System Manager; Responsible for all system management, daily operations, and

hardware maintenance of VAX-11/780 system aboard USNS Vanguard.

Education

New York University/Polytechnic Institute

Master of Science in Computer Science

Clarkson University

Bachelor of Science in Electrical Engineering

St. Bonaventure University

Pre-engineering Program

NY, NY

Graduated 2010

Potsdam, NY

Graduated 1984

Olean, NY

Transferred out in 1982

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