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Research Software Engineering (RSE)

RSE Service Request

 

Research Software Engineering (RSE) Services

 

Scientific Software Packages and Data Services

  • Design, development, optimization, deployment, maintenance of scientific software packages and data services
  • Development of
    • Data Science/Machine Learning/Deep Learning/AI apps and platforms
    • data-intensive and big data platforms
    • scientific packages (Python, R, C++, Fortran, MATLAB ...)
    • data acquisition and analysis automation platform
    • functional and robust UI/UX
    • microcontroller programs (Arduino, Teensy)
  • Add critical features to existing codebases
  • Improve the performance of existing software packages and optimization of scientific codes
  • Maintenance of the current codebases developed by researchers

 

Systems Design for RSE Projects

  • Architecture (storage, compute, networking, VM, database, backup/archiving, web/app server, load balancing, failover)
  • Data
  • Services & Components
  • Integration
  • Technology (infrastructure, systems, applications, components, toolsets, libraries, and APIs)
  • Information Security (Authentication, Level 3, Level 4, FISMA)
  • Deployment (FASRC Cluster, Azure, AWS, GCP ...)
  • Constraints

 

Consultation

  • Development of research software and data services
  • Domain-specific consultation on scientific software development
    • Parallel scientific computing (GPGPU, MPI, OpenMP, OpenACC)
    • Machine Learning / Deep learning
    • Advanced data visualization (VisIt, ParaView, Tecplot, yt)
    • Advanced numerical simulation
    • Compilers optimization
    • Biochemistry & Biophysics
    • Statistical mechanics
    • Many-Body theory
    • Astrophysics
    • Numerical relativity
    • CFD (MHD)
    • Finite Element Analysis (FEA)
    • Theoretical/computational nuclear physics
    • Molecular Dynamics (MD) and molecular modeling
    • Computational multiphase fluid dynamics and heat transfer
  • Joint grant submission on research software and data services development

 

Training

  • Research software development (Python, R, C++, Fortran, MATLAB ...)
  • Data Science, Machine Learning, Deep Learning, and AI tools development practices
  • Development of data-intensive and big data applications on the FASRC cluster
  • Numerical simulation code development

Training Calendar

 

RSE Group Current and Past Projects

 

Operant Conditioning Software

The Operant Conditioning (OpCon) software has been developed by the FASRC-RSE team to help researchers in Ölveczky lab with animal behavioral studies and to help them to better understand the brain motor skills. The software can be deployed to other labs and institutions. The hardware components are inexpensive compared to other commercial behavioral boxes which makes it a perfect choice for animal behavioral studies by researchers at Harvard and other institutions.

RSE_OpCon

Spike Sorting of Extracellular Recordings Software

The FASRC-RSE team has been developing a new parallel spike sorting software package to sort extracellular recordings for researchers in Ölveczky lab. The recordings are collected by 128 electrodes (batched in groups of 4 in 32 tetrodes) and record at 30 kHz yielding ~1 TB of data per day per subject. The FASRC CANNON cluster storage and computational power have been utilized for this project.

RSE_Ephys

 

Motion Capture Annotation Software Packages

FASRC-RSE team developed two software packages for motion capture experiment for Ölveczky lab researchers. The software packages are,

  • Frame Annotation Tool (FATGUI): A MATLAB graphical package to annotate video frames with a list of different behaviors. The software scans frames in the video and adds user tags to a MATLAB MAT-file. The annotations are used to train neural networks to predict animal behavior.
  • t-SNE Annotation Tool (t-SATGUI): A MATLAB graphical package to annotate points in the t-SNE map. The software plays recorded videos for each point, and the user tags different behaviors.

t-SATGUI

 

Secure Data Platform for Harvard HSPH Researchers

FASRC-RSE team has been working to develop a secure data platform and data services to support the data engineering needs of Professor Francesca Dominici's group at the Harvard School of Public Health. The data platform will host data from various governmental and non-governmental sources including high-resolution air pollution exposure data, census data, and health data from Medicare, Medicaid, and private insurance companies. The goal is to develop and implement systems and data services that can be used to efficiently query data at a variety of spatial and temporal resolutions to meet the needs of a large and diverse network of collaborators.

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