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Articles tagged: sysadmin
Mascot security – guest users and administrators
Mascot Security is a role-based access system that allows administrators to control different aspects of privacy and priority access. It integrates with authentication systems like Microsoft Active Directory (AD) and various single sign-on systems. It can also be configured for a core lab, where search results can be shared with collaborators without them having access to the results of other groups. [...]
Get more search speed with SplitNumberOfQueries
Mascot Server has several parameters and options that have an effect on database search duration. One of them is SplitNumberOfQueries, which specifies how many queries (MS/MS spectra) are searched at a time. The default is 1000 queries, which is reasonable, but like all defaults, it isn’t optimal. On most hardware, increasing it to 2000 will yield an immediate 10-20% performance [...]
Downloading UniProt proteomes via new API
The UniProt website received a snazzy facelift in June 2022. Both the browser interface and the REST API were updated. The previous version, now termed legacy website, remains available until the 2022_04 release under a new URL (https://legacy.uniprot.org/) – so there is limited time to compare and admire the improvements! The new API is an almost seamless transition for Mascot [...]
Mascot cluster installation security on Linux
Mascot Server has a built-in cluster mode, where the database search can be executed in parallel on a networked cluster of PCs. This requires no special hardware or operating software. The cluster can consist of ‘commodity’ PCs running Windows or Linux. Cluster mode is usually the most practical option for licences of 5 CPU or more, as discussed in Mascot [...]
Single sign-on (SSO) and Mascot
Mascot Server has a role-based security system called Mascot Security. Common use cases are restricting access to configuration files or specific sequence databases, or imposing limits on search size or duration for specific users or groups. These were discussed in earlier blog articles Mascot Security: priority settings and Mascot Security: privacy settings. Mascot Security isn’t designed to have super secure [...]
The minutiae of database management
The two major inputs into a database search are sequence databases and mass spectrometry data. Management of the databases in Mascot Server has evolved and improved over the years and newer versions. There are still a few issues that come up regularly and I am going to cover them in this article. Common error messages When you activate a new [...]
How to set up remote working
There are times when you unexpectedly find yourself having to work from home. Fear not: data analysis doesn’t need to stop when you’re away from the lab. Mascot Server has a client-server architecture, and the client PC can be located anywhere. Distiller and Daemon can also be used remotely, or they can be run on a remote client PC and [...]
Disaster recovery
There are a number of potential issues that can cause your Mascot Server or other computer infrastructure to stop working. In the worst case, you may need to do a full recovery from backups. This can be an involved procedure, but it is straightforward as long as you have backed up key configuration and data files. For disk or storage [...]
Spring clean your mascot.dat
Updates to Mascot 2.5 will be going out shortly. When an existing installation is updated, settings in the options section of mascot.dat are only modified by the installer in exceptional cases. The assumption is that any changes have been made with good reason and should be honoured. The down-side of this approach is that values may be persisted that are [...]
Backing up your Mascot Server
The demise of Tranche, last year, with reports that 80% of the raw data ‘safely held’ there has been permanently lost, should be a wake-up call for many laboratories to consider their back up strategy. It’s very hard to get reliable data for the annualised failure rate (AFR) of disk drives, but most estimates suggest around 1.5% of drives will [...]