This paid-for advertorial by CDD Vault appeared in the DDW / ELRIG UK Drug Discovery 2021 supplement in DDW Volume 22, Issue 4 – Fall 2021
For any research-based organisation in the life sciences arena, experimental data is the key to deriving biological and biochemical insight and understanding, and ultimately driving product development. The ability to manage, access, share – where appropriate – and anayse data is thus critical at all levels of research, from discovery, through development and into the clinic.
And with vast volumes of information being generated through diverse experimental workflows, and the need to manage huge volumes of samples and compound libraries and screening results, for example, managing all these different datasets using traditional spreadsheet-, or even paper-based approaches, is untenable. At VIB, a major non-profit research institute in Belgium, the group of scientists who carry out high throughput screening (HTS) assay development and HTS campaigns for both in house and partnered projects, implemented Collaborative Drug Discovery’s CDD Vault registration system and electronic laboratory notebook (ELN) as the central data management infrastructure that helps to maximise the value of the institute’s key compound library assets, track and compare experimental workflows, access data for analysis and comparison, and reduce repetition.
VIB is an entrepreneurial research institute focused on strategic basic research in life sciences. The organisation and its 1500 or so scientists work in close partnership with the five universities in Flanders – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel and Hasselt University – to expedite research and biological/biomedical innovation. It’s a strategy that has resulted in some ground-breaking discoveries, leading to the spinout of multiple companies to commercialise new platforms and technologies.
VIB has established core facilities to provide support in a wide array of technologies with the aim to advance science and accelerate breakthroughs explained Dominique Audenaert, head of the VIB Screening Core. “We have, for example, a Nucleomics Core that supports transcriptomics research, a Proteomics Core, an Imaging Core, and also the Screening Core that I lead. The small group of scientists in this Screening Core are focused on assay development – primarily to aid miniaturisation and automation of bench-top assays – and carry out the HTS programs”, Audenaert continued. “We run biochemical assays and cell-based assays to generate data on how for example protein activity and marker gene expression are affected by compound exposure, as well as more complex, high-content imaging assays that can evaluate morphological changes in cells, and see more directly how a compound interferes with the expression, localisation or function of a protein in a cellular context.”
The VIB Screening Core historically managed its compound libraries – the internal VIB collection spans about 45,000 compounds – using spreadsheets, but relating any insight from screening programs back to those structures was a major headache, Audenaert continued. “The Excel spreadsheets and basic database that contained the structures of the molecules didn’t allow us to annotate any of the biological data coming from the screens to those structures,” Audenaert noted. “And this meant that there was no way to immediately see, compare or otherwise anayse relational data in the context of these compound structures.”
Realising that a better platform was needed to support its operations, in 2016 the VIB Screening Core adopted CDD Vault as a secure repository for its compound data. Importantly, the vault made it easy to tie key screening and other experimental data to the chemical structures. “We carried out trials to assess different software packages, and CDD Vault stood out as an easy-to-use, web-based application,” Audenaert explained. “As a small team of biologists, not chemists, it was important to have a relatively simple, plug-and-play tool that was straightforward to implement and roll out. Having CDD Vault as our compound repository means that now, when we have finished a screen and generated the data, we can link that data to the structures, to facilitate additional cheminformatics analyses, say, clustering or similarity analyses between lead compounds.” Centralising all the data also makes it more convenient to cross-reference across different screens, he noted.
Importantly, the CDD Vault is easy to manage on a daily basis. “Data can be exported manually out of the vault as files to chemists and other scientists.” This process can also be automated through the API, which is something CDD will be working on with VIB.
The VIB Screening Core’s remit and expertise have evolved from carrying out primarily plant-based screening in small model plants and plant cell cultures, to mammalian cell-based assays, and now high-content screens, Audenaert explained. “We started out carrying out primarily relatively simple, plate-reader-based assays, but have more recently been carrying high-content imaging screens, and that was actually quite a big step, with new scientists brought on board.” High-content screens also set more of a challenge with respect to data storage and curation, he continued. “We need to store and manage high volumes of images and image data, which adds another layer of complexity onto the screening data. We currently use PerkinElmer’s Columbus image data storage and analysis system to manage those images.”
One of the next potential steps for VIB will be to connect the Columbus platform with CDD Vault, so that the image data can be linked directly back to the compound structures. This is something that can be done using CDD Vault API.
The VIB Screening Core has also, more recently, implemented the CDD Vault ELN, so that the scientists can securely, and accessibly record and report experiments and laboratory workflows, Audenaert noted. “The Vault represents the repository for our screening data, but we also want the ability to track the experiments that are carried out during assay development. We can now put these experiments and workflows directly into the ELN. The ELN is a relatively recent implementation, but the benefits are evident. Our scientists no longer have to rely on remembering when or how a past experiment was carried out and can search and access the ELN easily. All experimental data and workflows can thus be tracked, we can learn from past projects through a complete trail of activity and documentation, use the information to translate past experiments into new studies, and ensure that we don’t repeat past work unnecessarily.”
The CDD Vault registration system and ELN have formed a key infrastructure that is allowing the VIB Screening Core to digitalise its laboratory, streamline and maximise the value of data emerging from assay development, and HTS campaigns. “These new tools have significantly boosted our efficiency and the intelligence and insight derived from our in-house projects and assay development efforts, as well as maximised the depth and breadth of data and value chain, for our external partners and collaborators,” Audenaert suggested. One of VIB’s key strengths is its flexibility to work with partners in a wide range of fields. “We apply our expertise to many different fields of research and experimental goals,” he continued. “We can work with industry on a collaborative basis to generate shared IP, but can also offer our expertise on a fee-for-service basis. The business and commercial support of VIB allows us to tailor partnerships on an individual basis. CDD Vault and its ELN represent key tools that can only aid that flexibility, and help to maximise value chain from our research carried out by our own scientists, and on behalf of and in partnership with an increasing number of collaborators and clients who access our expertise.”