Open-Source Bioinformatics Software Consultant

For further inquiries regarding the following opportunity, please contact one of our Talent Specialists: Arun | 224-507-1292 Amit | 224-507-1290 Title: Open-Source Bioinformatics Software Consultant Location: Remote Duration: 3 months with possible extension 30 hours per week, Monday through Friday. Description 1.0 Background

• The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand challenge of systems biology-predicting and designing biological function at scales ranging from the biomolecular to the ecological.
• KBase enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions, perform extensive analyses on scalable computing infrastructure, and combine experimental evidence and conclusions to model plant and microbial physiology and community dynamics.
• Metabolic modeling is a key feature used by many KBase users, with thousands of metabolic models reconstructed using KBase to date. To maintain and enhance this capability, KBase needs to rely on fully open-source software for deploying metabolic modeling tools with no use restrictions.

2.0 Scope

• This project aims to advance the Client's mission in leadership in metabolic modeling research by enhancing the KBase platform's computational capabilities, specifically in the area of metabolic modeling.

3.0 Objectives The primary objectives of this contract effort are to:

• Research and review relevant open-source cheminformatics software
• Benchmark the performance of available open-source software
• Implement and wrap best-performing software in KBase
• Provide more accurate Gibbs free energy predictions
• Expand current capabilities and introduce new features to KBase users

4.0 Tasks and Delivery (Job Description) The contractor will be responsible for:

• Conducting comprehensive research on available open-source metabolic modeling software
• Performing benchmarking tests to evaluate the performance of identified software
• Implementing selected software into the KBase platform
• Developing wrappers for the best-performing software to integrate with KBase
• Documenting the implementation process and providing user guides
• Collaborating with the KBase team to ensure seamless integration of new features
• Providing regular progress reports on the development and implementation process

Deliverables:

• Weekly progress reports
• Benchmarking results and analysis
• Implemented software and wrappers in KBase
• Documentation and user guides for new features
• Final report summarizing the project outcomes and recommendations for future improvements

5.0 Required Knowledge, Skills, and Abilities

• Experience with cheminformatics modeling and related software
• Proficiency in programming languages commonly used in bioinformatics (e.g., Python, R)
• Familiarity with open-source software development practices
• Strong analytical and problem-solving skills
• Excellent communication and documentation skills

6.0 Task and Time Reporting

• Timesheets will be submitted on a weekly basis and will be approved by the supervisor accordingly.

7.0 Government-Owned Property

• To be determined based on specific project needs.

8.0 Security Requirements

• The contractor may require remote access to Client machines and KBase development environments. Appropriate security clearances will be necessary.

9.0 Computer Protection Program

• The contractor(s) may have root access to government computers and/or Business Information Systems.
• The contractor(s) shall adhere to all policies and procedures of the Client Computer Protection Program, must not bypass any procedures established to protect data, applications, hardware, or communications at Client, must maintain a work environment that will satisfy audit, privacy, and protection requirements, and must report any findings of inadequacies to the technical contact and the Client Cyber Security Representative.

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