Skip to main content

Software Engineer – Chemoinformatics

Software Engineer – Chemoinformatics

Job ID 5554
Job Location Rockville - MD
Full-Time/Part-Time Part-Time

The Software Engineer – Chemoinformatics provides support to the U.S. Food and Drug Administration (FDA). This position maintains and enhances the process of serialization of public substance data from the Substance Registration System (SRS) and Global Substance Registration System (GSRS) into Substance Index Structured Product Labeling (SPL) files. The Software Engineer – Chemoinformatics develops a modern data management environment based on the Health Level Seven (HL7) version 3 Reference Information Model (RIM) for managing the information received from the regulated industry and the public. The data management environment includes the HL7 Data Exchange Services that include a source database for storing data and services for the automated receipt, loading and retrieval of the data.



Essential duties and responsibilities include the following.  Other duties may be assigned.


Responsible for the integration of CNI Core Competencies into daily functions, including: commitment to integrity, knowledge / quality of work, supporting financial goals of the company, initiative / motivation, cooperation / relationships, problem analysis / discretion, accomplishing goals through organization, positive oral / written communication skills, leadership abilities, commitment to Affirmative Action, reliability / dependability, flexibility and ownership / accountability of actions taken.


Uses the FDA provided representative subset of public substances in JSON format, the current code of the SRSutil software with comments, the SPL and the implementation guide for substance indexing to convert substances from JSON to SPL format.


Reports what types of substances can/cannot be converted. Suggest what modifications to the SPL data model or to the SRSutil software are necessary. Estimates the conversion rate.


Stores data in the JavaScript Object Notation (JSON) format. Analyzes the format and makes sure it provides all the data necessary for generating SPL files.


Creates modules that reads data in GSRS JSON format. If GSRS JSON is missing data necessary for producing SPL files, works with GSRS team on adjusting GSRS JSON format. Creates a module(s) that reads the data.


Modifies SRSutil software to accept the updated SPL model. Modifies SRSutil software to cover conversion of polymers, nucleic acids, non-stoichiometric chemicals, complex cases of proteins and structurally diverse substances


Serializes substances into SPL format. Reports conversion errors in the SPL files.


Works with FDA on developing testing metrics. Uses the metrics to evaluate conversion quality. Identifies conversion errors due to bugs in SRSutil software.


Identifies conversion errors due to errors in data and calculates the conversion rate. Fixes bugs in SRSutil software that caused conversion errors.


Identifies and mitigates risks to the Government. Maintains continuity of operations, establishes communication, and establishes schedules and tasks.


Assist with the software/data Transition-In plan approved by the Government.


Creates a transition completion report showing final status, remaining issues and risks.


Provides support with tasks including, but not limited to, committee meeting agenda preparation and distribution.

Responsible for aiding in own self-development by being available and receptive to all training made available by the company.


Plans daily activities within the guidelines of company policy, job description and supervisor’s instruction in such a way as to maximize personal output. 


Responsible for keeping own immediate work area in a neat and orderly condition to ensure safety of self and coworkers.  Will report any unsafe conditions and/or practices to the appropriate supervisor and human resources.  Will immediately correct any unsafe conditions to the best of own ability.



Bachelor’s in Computer Science, Chemistry or related field of study, and minimum of three (3) years’ experience in Application Development.  Experience developing Chemo-Informatics algorithms and analytical tools for medicinal chemists. Experience and format proficiency in Spartan molecular modeling and computational chemistry software such as ChemDraw, Symyx Draw, CACTVS, Open Babel, Molfile, SMILES, InChI, Wisswesser Line Notation. Experience creating and managing C# applications using Oracle and SQL*Server databases is required. Familiar with JSON format.





Working knowledge of HL7 based standards

Ability to develop and manage desktop and web applications using HTML5, XML, Java Script, jQuery, JSON, .Net Framework, AJAX, CSS, VB.Net, C# and Microsoft MVC Framework using CMS tools like SharePoint and Visual Studio

Working knowledge of hash codes for representing chemical structures

Working knowledge of Cheminformatics toolkits such as Indigo and Mathematica

Knowledge of how to prioritize workflow required

Ability to project a professional image in all interactions with clients, vendors, and staff 

Ability to handle stressful and demanding situations without disruption of efficiency or professional demeanor

Ability to work flexible hours according to business demands; sometimes on short notice

Ability to conduct research using the Internet and must be familiar with Social Networking

Ability to develop and maintain custom applications, providing technical documentation, coding to industry standards, and team oversight

Ability to analyze and troubleshoot services for complex problems, recommend improvements, and stay up-to-date on security vulnerabilities, new features, hardware, software, and feasibility determination 



Ability to calculate figures and amounts such as discount, interest, commission, proportions, percentages, area, circumference and volume. Ability to apply concepts of basic algebra and geometry. 



Ability to define problems, collect data, establish facts, and draw valid conclusions. Ability to interrupt an extensive variety of technical instructions in mathematical or diagram from and deal with several abstract and concrete variable.



Ability to read analyze and interpret common and technical journals, financial reports, and legal documents. Ability to respond to common inquiries or complaints from customers, regulatory agencies, or members of the business community. Ability to write speeches and articles for publications that conform to prescribed styles and format. Ability to effectively present information to top management, public groups, and / or boards of directors.