![]() ![]() ![]() MSBio is a very complex project and we are glad that we are now able to provide a convenient way for bioinformaticians to easily install the images containing both third-party tools and databases. Fortunately, most key databases such as Gene Ontology, Entrez, STRING, EggNog are free to everyone, so MSBio analyses remain rather comprehensive than most other solutions. Therefore, we need to go with a conservative minimum subset of data sources and restrict MSBio for non-commerical use (commercial users, please read on) in our licensing terms. ![]() Although most data providers are okay with web portals providing a nibble of their data for each analysis, as it is probably viewed as a free advertisement, redistributing the their database is certainly not in the consideration. First, we are not lawyers ourselves to interpret every lines of legal statements. As we cannot afford to have MSBio connect to our central database, we need to distribute databases with MSBio as well. CYTOSCAPE VIRAL CODEMetascape relies on over 40 databases, therefore, simply installing all Metascape code does nothing for users. Our suggestion is either convince your IT team to let you run Docker on your in-house Linux servers, or you can install Docker for your own Linux, Mac (except M1 chip), or Windows machine.Īnother big hurdle for MSBio is the underlying databases. We are sorry for users do not have a Docker infrastructure. Instead of virtual machines (VM), the new technology enables such images to be delivered in the form of Docker images. The only alternative is to distribute MSBio almost as a preinstalled machine image. There will never be a standalone MSBio installation package due to these reasons. If we released a package, we would have been flooded with installation questions and could not breathe. CYTOSCAPE VIRAL SOFTWAREWhy not release Metascape as an R package, some asked? This is not feasible, as users will not only need to install tons of software libraries (many require compilations), but also database servers, third-party tools including Cytoscape and Circos (using Perl unfortunately), etc. Thus, we have to reserve our server for biologists’ use and cannot afford to expose it as the world’s shared computational hardware. Despite we have the best computer algorithm specialists in our team, Metascape is much more resource hungry than most other gene list enrichment services. Why not provide Metascape Application Programming Interface (API), you asked? To obtain the comprehensive analysis results, Metascape utilizes computationally-expensive algorithms and visualization tools. Frequently computational users have made inquiries regarding their desire to run Metascape analyses programmatically. The reality is that the analyses implemented behind Metascape are not only difficult for biologists to perform, but also quite challenging for many bioinformaticans to implement. Metascape was initially designed to support biologists, as we observed most gene-list analysis tools were bioinformatician-oriented rather than biologist-oriented. We are extremely excited to make MSBio available to the bioinformatics community, including a commercial license option for for-profit entities (this post was updated on Dec 5, 2021). ![]()
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