Ray Tran | BEng
Head of Instrastructure
Elixir Software
The Science of Software Infrastructure: Why We’re Writing This Series
Scientific research is built on precision, collaboration, and efficiency. But when it comes to the software infrastructure that supports these critical workflows, things are often less than ideal. Too many research organizations rely on legacy systems, brittle pipelines, and deployment processes that aren’t designed for scale, security, or flexibility.
At Elixir Software, we specialize in building scientific workflow solutions that eliminate bottlenecks, improve visibility, and ensure that research teams can focus on what they do best: advancing science. Our work has shown us firsthand how modern infrastructure can transform how scientific teams operate. However, technology doesn’t stand still—and neither can we.
This blog series is about the process of modernizing scientific software infrastructure: the tools, techniques, and philosophies we’re applying to build scalable, secure, and resilient solutions for research-driven organizations.
Who should read this?
If you work at the intersection of science and software, this series is for you. We’re writing for:
- Scientific Leaders and Research Teams – You might not be deep in the weeds of cloud infrastructure, but you care about reliability, security, and performance. You want software that works when you need it, every time.
- Software Engineers and DevOps Professionals – If you’re navigating the challenges of deploying and maintaining infrastructure for research environments, we’ll be discussing real-world solutions to real-world problems.
- Platform Engineers & Team Leaders – A strong foundation isn’t just about technology, but also about how teams work together to roll out and sustain these improvements. We’ll be exploring team structures, cross-team interactions, and metrics like MONK to measure developer adoption and engagement.
Why are we writing this?
We’re not just upgrading our stack for the sake of it. Scientific software infrastructure is often an afterthought, which leads to slow deployments, unpredictable downtime, and security risks. We believe that by adopting best practices from modern cloud architecture, we can:
- Make scientific software more resilient – Cloud-agnostic, multi-AZ deployments, and self-healing systems ensure research workflows keep running, no matter what.
- Ensure continuous availability – Zero-downtime deployments and automated failovers mean fewer disruptions.
- Enhance security – Scientific data is valuable and often sensitive. We’re implementing stronger security frameworks to keep it safe.
- Improve developer experience – We’re using GitOps to automate infrastructure deployments and reduce the time it takes to deliver new features and fixes.
- Scale intelligently – Scientific research is dynamic. Our infrastructure must handle variable workloads efficiently.
- Build the right teams to support all of this – None of these improvements matter if they aren’t supported by a well-structured team. We’ll explore best practices in team organization, cross-functional collaboration, and measurement frameworks to ensure adoption and success.
What's coming next?
Over the next few posts, we’ll break down how we’re implementing these improvements, including:
- Resilience – Designing failover systems that can withstand disruptions.
- Zero-Downtime Deployments – How we’re rolling out updates without interrupting researchers.
- Security Enhancements – Best practices we’re applying to protect sensitive data.
- GitOps in Action – How we’re using automation to streamline software updates and infrastructure changes.
- Scaling for the Future – Lessons learned in building infrastructure that grows with the needs of scientific teams.
- Team Structure & Cross-Team Collaboration – Exploring how effective team structures enable success in rolling out and maintaining these improvements. We’ll also discuss MONK metrics to measure developer buy-in and engagement, ensuring that infrastructure changes are embraced rather than resisted.
We’re not just improving our own stack - we want to share what we learn along the way. If you’ve ever had to balance cutting-edge research with cutting-edge software, we think you’ll find something useful here. Welcome aboard.
Ray
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A US-based global biotechnology company had a commonly seen challenge in Laboratory Animal Science (LAS). Biopharmaceutical LAS teams receive multiple project requests for studies and need to schedule the delivery of tasks by relevant skilled technicians, with the available and designated time slots. In conversation with their clients, Elixir learned that many of the currently available tools used for LAS are disconnected and inefficient for effective study planning, tracking and delivery. The use of multiple emails, calendars and isolated files e.g., spreadsheets has resulted in a complex process, that is typically maintained through time-consuming daily meetings.
The challenge: This clinical-stage biopharmaceutical company’s chemistry engine combined in-house medicinal chemistry design with external synthesis capabilities. It was critical for them to have a robust process for tracking the design cycle (Design-Make-Test-Analyze) to assure expedient execution and quality decision making. A specific technical challenge, common to many institutions, is unambiguous tracking of synthetic targets across multiple projects and partners. Issues may and do arise from keeping track of the target status, changes in the target priority, and other synthetic queue modifications.In common with many growing biotech companies, a Boston-based biotech augments its in-house chemistry team with tens of synthetic chemists from multiple CRO partners. While this enables the company to significantly increase its capacity, it also brings the challenge of coordinating work between multiple organizations around the globe. “We were relying on emails to exchange information, which ended up either in PDFs buried in a file share or in people’s memory. It was difficult to keep track of who was making what, or to find out if something had been done before, which meant that people at different locations were working on the same target and some compounds were re-proposed unnecessarily. There was also the risk of timelines sliding because an important compound went under the radar and wasn’t worked on in a timely manner”. Director of Informatics, Boston-based biotech The solution: Aware that current methods of working might be improved by using an electronic tool to track and manage synthesis, the team looked for a solution. It turned out that they were not alone as a colleague from another company suggested they look at chemTraX. The initial demo was well received, so the next step was to conduct a hands-on evaluation of the system. Regular feedback throughout ensured that the configuration met the desired synthetic chemistry workflow and was ready to be rolled out to the wider chemistry team, both internally and to key people at its CRO partners. The results: “chemTraX has enabled us to achieve a truly distributed drug discovery process. The visual status board provides clarity and ensures everyone is on the same page when it comes to priorities and knowing what needs to be made, by who and when. Our CRO partners update the status of their work directly in chemTraX and add comments if needed, which not only means we always have up-to-date information but also facilitates communication during weekly meetings and mitigates potential issues with language differences. The information managed by chemTraX has provided us with a fantastic knowledge base that we can use to understand why a given compound was or wasn't made and reduces the chance of duplicating effort. chemTraX has become an integral part of our informatics ecosystem and is fundamental to the way our chemists work”. Director of Informatics, Boston-based biotech
The challenge: This clinical-stage biopharmaceutical company’s chemistry engine combined in-house medicinal chemistry design with external synthesis capabilities. It was critical for them to have a robust process for tracking the design cycle (Design-Make-Test-Analyze) to assure expedient execution and quality decision making. A specific technical challenge, common to many institutions, is unambiguous tracking of synthetic targets across multiple projects and partners. Issues may and do arise from keeping track of the target status, changes in the target priority, and other synthetic queue modifications. The solution: While solutions to these common problems exist at large pharma companies, and are typically proprietary, the selection of tools for smaller biotech companies is limited. “We heard about chemTraX from one of our partners and were excited to give it a try. It turned out to be a tool which met many of our needs: unambiguous tracking of synthetic targets across multiple projects/CRO partners, flexible customization to meet our project objectives, and ease of implementation. Among other benefits, it should be mentioned that the implementation team were very attentive and responsive to our needs. Robust control of access privileges for CRO partners was implemented natively within the application." Director of Chemistry, clinical-stage biopharmaceutical company The results: The company now has an accessible and unambiguous system for synthetic target tracking which eliminates target duplication and ambiguity, greatly simplifies management of multiple chemistry CRO partners, and provides an up-to-date status of the synthetic queue. “We are excited about the prospect of further integration of this tool in our chemistry workflow.” Director of Chemistry, clinical-stage biopharmaceutical company
New molecule design incorporating 3D, chemical property and nearest neighbor information (left, Torx Design) is connected to hypothesis tracking that enables project teams to track and manage synthetic chemistry efforts (right, Torx Make). Cambridge, UK – 22 April 2020 – Torx Software announces the launch of Torx, a new web-based platform for small molecule discovery chemistry. Torx enables chemists to work together, share ideas, manage resources and track progress in the Design-Make-Test-Analyze (DMTA) workflow. Molecule design, review, prioritization, resource allocation and synthesis scheduling are separate parts of a complex process that can lead to productivity bottlenecks and slow the drug discovery process. Torx deploys dedicated applications within medicinal chemistry workflows to reimagine the end-to-end process and create a team-friendly, productivity-centric approach. Coupled with enabling research managers to manage synthesis resourcing and prioritization, Torx can reduce time to quality candidate selection by working through DMTA cycles faster and more efficiently. “Torx connects the discovery process across teams in different locations,” said Dr Tim Cheeseright, CEO, Torx Softwae, “Torx provides an information rich environment for small molecule design combined with detailed scheduling and management of synthetic chemistry. Chemists can share knowledge and ideas. Project managers can track progress and resources, all from the same software platform.” “We are delighted to launch Torx to the chemistry community bringing together key technologies from both Cresset and Elixir into a single DMTA workflow application”, said Dr Paul Faulder, CEO, Elixir Software. “This ground-breaking platform will facilitate increased efficiency of chemistry teams and their partners around the world working towards their next clinical candidate.”
July 2020 sees the launch of a brand new responsive, mobile-ready website for Elixir Software, putting more information about our tracking and collaboration software in the palm of your hand.
