Data-management software provider IDBS is looking to parlay its strong position in high-throughput screening into an advantage in the nascent high-content screening market.
IDBS, based in Guildford, UK, recently announced that the Institut Pasteur Korea, a research center at the Korean Institute of Science and Technology in Seoul, will use its flagship ActivityBase software to manage both HTS and HCS data.
IDBS’s experience in the HTS data-management space, in which it currently has deals with 18 of the 20 top pharma companies, could give it an advantage in the HCS market, where potential competitors include Cellomics, Genedata, Definiens, BioImagene, and Vala Sciences.
Laurence Painell, product manager at IDBS, said that while “a number” of IDBS customers are already using ActivityBase to store high-content data, the Institute Pasteur Korea is “the first client of ours to really crunch large volumes of high-content screening data through ActivityBase.”
The IP-K team has “built Excel templates to gather data and perform the curve fitting on the different channels that come off the high-content data, and then process that and put it back into the ActivityBase database,” Painell said.
Thierry Christophe, head of the screening and pharmacology lab at the institute, said in an e-mail to BioInform’s sister publication Cell-Based Assay News that his lab has developed its own software to interpret images obtained with its Evotec Opera automated confocal microscope. According to the IP-K website, the Christophe lab uses disease-based cell models to screen libraries of more than 100,000 molecules.
“The software interprets the image and gives numeric results, which are then processed using ActivityBase,” Christophe wrote.
Christophe noted that the primary difference between HTS and HCS data is that each image in a high-content screen provides more than one numeric result. “Indeed, from one picture, we can obtain information on the compound activity but also its cellular toxicity, sometimes some internal controls as well. This means that we obtain many different numeric results per well.” For each well, Christophe’s lab measures an average of two to five different parameters, and the time required to analyze the image increases with the number of parameters, he noted.
During a typical screening campaign, he wrote, “we produce around 35,000 to 38,000 pictures per day and in most cases, these pictures are analyzed during the night following the screen.” Another challenge, he noted, is storing the images. “For this, we have huge hard disk systems, but it is still a question for the future.”
Christophe said in his e-mail that his group is using ActivityBase “to store and manipulate the numeric data coming from the image analysis (or from more classical readout when applicable).” The lab is also using IDBS software for compound registration and for compound and plate management.
The IP-K team stores data on compound activity and toxicity in ActivityBase, and plans to develop its own query system to get “direct access to multiple information” in compound databases, Christophe said.
Pannell told Cell-Based Assay News that some customers who do rely on ActivityBase for HCS are able to use it “out of the box,” but most require some degree of customization.
“The thing with HCS is that it’s a bit like FLIPR used to be: people are doing a lot of different things with it,” he said. “Some ask us to write extensions, some use it as is, and some will write their own extensions.”
Painell added that ActivityBase provides flexibility for users. “They capture the data, get it into Excel, then they can do whatever they want with their programming — but then it goes back into a database,” he said. “We do the data-management platform, where they can do their own things that they think give them a proprietary advantage.”
Building on the Base
IDBS’s installed base in pharma could prove useful as the company faces competition from software providers who specialize in high-content screening data. Cellomics, for example, markets the Cellomics Store platform for storing and managing HCS data. Other vendors, such as Genedata, Definiens, BioImagene, and Vala Sciences, offer a range of software packages for HCS data analysis and visualization.
But Glyn Williams, vice president of marketing and product development at IDBS, said that the company expects HCS customers to use ActivityBase in concert with one or more of these packages.
“Some of our customers use ActivityBase to collect the data, then maybe use Genedata on top of it, and then use ActivityBase to put the data into the database,” he said.
“The thing with HCS is that it’s a bit like FLIPR used to be: people are doing a lot of different things with it.”
“In some cases people may use specific tools, and maybe use Spotfire, as well, on the data, but they nearly always use ActivityBase to get the data in, do some of the initial QC, and then maybe do some of the mining and trend analysis, and still use ActivityBase to come back to the data at any time,” Williams added.
Depending on the application and the specific workflow, he said, other HCS packages “can be viewed as competitive, and in some cases they can be viewed as complementary.”
Painell noted that ActivityBase does not provide image analysis capabilities, so users will likely turn to a third-party package for that step. “A lot of our other customers have Cellomics, and that’s exactly the way that they use ActivityBase in conjunction with Cellomics, so it’s very complementary,” he said.
IP-K’s Christophe said that he considered other commercial data-management systems for the screening center, but finally opted for ActivityBase “as I knew this system from my previous positions and I knew what we could do with it.”