Core Facility Software Development Needs

--- description: Report from interviews author: James Collier tags: proposal --- # Core Facility Software Development Needs This document outlines the broadly applicable software development needs of VIB Core Facilities, Tech Watch, and Technology Training. Interviews were conducted with these facilities: * **Screening Core** (Dominique Audenaert, Vera Goossens) * **Metabolomics Core** (Geert Goeminne) * **Proteomics Core** (Francis Impens, Teresa Maia, Sara Dufour) * **Bioimaging Core** (Jari De Vuyst) * **Tech Watch** (Wai Long Tam) * **Technology Training** (Alex Botzki), and * **Data Core** (Frederik Coppens) ## Yet to meet * Single cell core * Flow core Leuven * Protein core * Nucleomics core * Metabolomics core Leuven * Flow core Gent * Flow core Leuven ## Background These interviews involved workflow observation and probing for places where software can help improve efficiency, accuracy, or cost. ## Goals The goal of software development is to provide automation to facilities that will assist in them completing their work quickly, accurately, and cheaply. To this end, software developed for the VIB Technology program should: * Be broadly and generally useful to several core facilities. * Provide substantial value in terms of time or cost savings. * Integrate with existing software and data facilities already used by VIB generally. ## Customer Reporting The Screening, Proteomics, and Metabolomics core facilities employ bespoke reporting tools that have a large overlap in required features. * [Spotfire](https://www.tibco.com/products/tibco-spotfire) * [Phantasus](https://phantasus.vib.be/) * Custom reporting pipelines Despite the large overlap in required features little or no functionality, knowledge (each core is mutually unaware of how the others are generating reports), or existing VIB services (such as Connect) and infrastructure is shared between each of these solutions. Furthermore, the Data Core is developing a metadata platform that could provide the necessary basis for a common reporting service. The essential features of reporting tools are: * Data import and tracing (when, where, who). * (Interactive) plotting and data analysis. * Customer isolation and authentication. * Share reports with customers. A common customer reporting tool would meet all required goals by being generally useful by multiple facilities, save time and money by sharing features needed by all cores and be extensible for other required features, and integrate with existing VIB services (Connect, Metadata platform, E-Learning, ...) ## Text mining Tech Watch have a proof-of-concept system to mine text from press releases, venture capital, and patents in order to discover potentially useful new technologies. Currently, this is used to automate the process of monitoring the progress of the different fields and ensure that Tech Watch are up to date with the best tools for research/cores. The current proof-of-concept is not well integrated and requires a lot of manual intervention. This tool can be polished, automated, and opened to other facilities in order to highlight: * important/useful/interesting publications * press releases * patents * other related documents. It could also be used to monitor VIB startups and competition. Such a tool is broadly useful to at least Tech Watch and business and likely Core Facilities as well. It automates a time consuming task and could integrate well with other VIB services such as an interface provided through Connect. ## Training and E-Learning VIB Technology Training runs an "E-Learning" platform used by all of VIB. This platform is used to present and develop all of the training programs delivered by Technology Training and needs to expand to meet the needs of VIB generally and the vision. Notably, the required features are: * Interactive learning paths (this could be a standalone component made available to international collaborators, e.g. the Memorandum of Understanding with EMBL) * Integration with other VIB services such as training.vib.be * Multimedia integration The E-learning platform is broadly used by VIB core facilities to provide training to all of VIB. Any improvement in its operation has a large impact on trainers and on students. The platform also needs to integrate with existing services to operate and could be a source of international collaboration. ## Conclusions Every facility I spoke with has significant unmet software development needs -- even much beyond what are listed above. Furthermore, every core facility I spoke with are either developing some software internally to meet these needs or outsourcing software development. This is a very unfortunate situation that is not only leading to a huge waste of time and money, but also duplicated effort developing services that should be provided by VIB. ## Future work It is possible that all \*omics Core Facilities share similar reporting requirements making extension of the [Phantasus](https://github.com/ctlab/phantasus) application a potentially valuable investment. Therefore the following could be organised: 1. Meet with remaining core facilities, and have them demonstrate their workflow and ask about their software development needs. 1. ~~Meet with the Data Core about the metadata platform.~~