Scientific Software

ESI software solutions are easy to use and tailored to fit your unique scientific needs.

ESI Services

ESI’s software offerings run the gamut, from simple solutions to speed your workflow to highly tailored approaches that address a unique need, such as bridging the gap between computational biology and clinical research. Because our staff are also scientists, we understand those needs (e.g., we know where the bottlenecks occur, where accuracy is paramount, and where data bias might be a problem). Our staff has the scientific and technical know-how to develop software that solves highly complex problems within specialized areas, such as precision medicine. Most importantly, you don’t need to be a coder to use our products. We give you the solutions you need, often with a few clicks of a mouse.

Our software services include:

  • Software Development: Designing and developing proprietary software tailored to your needs.
  • Software Enhancement: Modifying existing software to better suite your work and to ensure security.
  • Quality Assurance: Testing and validating software and ensuring full certification.
  • Implementation and Technical Consultation: Launching software applications for large projects and individual tasks.

Our software services have also been appraised at a CMMI Maturity Level of 3. CMMI is a process improvement approach that provides organizations with essential elements of effective processes that ultimately improve their performance. 

What our CMMI Maturity Level 3 rating means for you:


 

  • We use organizational standards and tailoring to address project and work characteristics.
  • Our projects use and contribute to organizational assets.
  • We focus on achieving both project and organizational performance objectives.
  • We’re dedicated to continuous performance improvement and producing the highest quality of products and services.

ESI Solutions In Action

For nearly two decades, ESI has worked with federal clients, such as the National Cancer Institute (NCI), to develop software to address a scientist’s unique needs.

 

We’ve designed and implemented dozens of bioinformatics software and tools, including approaches to interpret genetic and proteomic data, longitudinal data, and other biomarkers of disease. Moreover, because we build in sophistication, even students and novices can use our tools with the same success as experts in the field. Over the years, we’ve developed more than 60 software packages. Recent examples include NCI’s cProSite, ForgeDB, and 3DVizSNP—all designed to operate using a series of drop-down menus and simple filters.

 

ESI’s expertise has helped launch key NCI initiatives, such as the Cancer Research Data Commons and the Childhood Cancer Data Initiative—complex ecosystems with petabytes of data.

 

CRDC specifically was launched to answer the Cancer MoonshootSM initiative’s call to accelerate the access and sharing of cancer research data, but it faced two key problems. First, it needed to support the full range of large-scale biological data (e.g., sequencing, proteomics, flow-cytometry, etc.). Second, researchers needed to have ready access to these data to help speed scientific discovery, which meant it needed to be fast.

 

ESI’s solution was to use “Bento,” an open-source software, which enabled us to launch a fully functioning data commons within 6 weeks. We built Bento work on both local servers and in the AWS and Google Cloud platforms. And, data access is role-based meaning that NCI was able to assign scientists different levels of access depending on their specific roles and needs, giving them the highest level of security.

 

Because Bento is modular, with each component fully tested and validated, it can support a range of data sets without the need for additional coding or lengthy testing. For example, both the Integrated Canine Data Commons and Clinical Trial Data Commons were launched with Bento despite having distinct data sets from different species.

 

Furthermore, our Bento model is schema-less, meaning it can be easily extended to accommodate new nodes and data types, without needing to tamper with the original model. You can learn more about the core data model and our extended BENTO_TAILORx on Github.

maintaining reliable access to lifesaving cancer prediction tool

In cancer research, making advancements to better public health is the goal. As a part of that effort, the National Cancer Institute’s Division of Cancer Epidemiology and Genetics built a state-of-the-art program called the Breast Cancer Risk Assessment Tool (BCRAT). This tool, which makes breast cancer risk assessment accessible to doctors around the world, has a simple interface that is easy to operate. By answering a series of personalized medical questions, users can estimate their risk of developing breast cancer in the next five years, as well as over their lifetime.    This medical advancement gained popularity in March 2024 thanks to an endorsement from actress Olivia Munn. In an Instagram post, she credited BCRAT for accurately predicting her cancer, touting it as a lifesaver. Her post sparked a surge in usage that the original infrastructure struggled to handle, leaving users unable to access this vital tool.   As part of our work for NCI, ESI’s development team handles the operations and maintenance of BCRAT, along with updates to the tool’s website and its Cloud hosting infrastructure. When the original infrastructure crashed, we made a quick fix and increased the size of the hosted instance, allowing users to quickly get back into the tool. To avoid further outages, we implemented a serverless architecture to auto scale the CPU instances as the calls increase – essentially the more people who access the tool, the more power the server will use to make the tool available. While this makes managing the increased user base easier, it also significantly saves on hosting costs.

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