Products: Biolinx (subscriber)

Thanks for subscribing to BioLinx! Depending on the subscription you have purchased (annual vs educational), you will recieve instructions to either install the system, or connect to our Biolinx server. For any general support questions, please contact us by email at

The IP address of our Biolinx server instance is If you bought the educational subscription, you will also recieve a login name and password. You can use these three credentials (IP address, login, password) and use a SSH program like Putty (download here) to connect to this server.

System Overview
The Biolinx operating system is CentOS, which is one of the flavors of open-source linux. Users log in into their home directories with a default shell as "bash". All the software (see list below) is installed under /usr/software. Multiple versions of the same software may sometimes be available. Software binaries must be added to the $PATH environment variable before being used, or called directly from their absolute locations. If you are not familiar with this, you should take a basic linux class or enroll in our linux training course. The examples and data used in the courses are under /usr/edu. You can copy them to your home directory with the cp -r /usr/edu/perl1 . command (to copy the "perl1" course scripts and data, for example). There are some public datasets available in the /usr/public_data directory. These should not be copied into your home directory, rather you can reference the data in this shared location.

Software available:

AllegroLinkage AnalysisOur GuideUser ManualWebsite
BedtoolsCreate genome interval filesOur GuideUser ManualWebsite
BlastSearch sequences in a databaseOur GuideUser ManualWebsite
BowtieMap and align NGS readsOur GuideUser ManualWebsite
BWAMap and align NGS readsOur GuideUser ManualWebsite
ClustalWMultiple sequence alignmentOur GuideUser ManualWebsite
CrossBowMap NGS reads and call variantsOur GuideUser ManualWebsite
CufflinksEstimate expression from TopHat aligned NGS readsOur GuideUser ManualWebsite
FastaSearching sequences in a databaseOur GuideUser ManualWebsite
Fastx toolkitManipulating NGS readsOur GuideUser ManualWebsite
MAQMap and align NGS reads, call variantsOur GuideUser ManualWebsite
MfoldDNA and RNA secondary structure predictionOur GuideUser ManualWebsite
PlinkLinkage analysisOur GuideUser ManualWebsite
PlinkSeqLinkage AnalysisOur GuideUser ManualWebsite
Primer3Primer designOur GuideUser ManualWebsite
PrinseqQuality of aligned NGS readsOur GuideUser ManualWebsite
SamtoolsVariant analysis of aligned NGS reads/td>Our GuideUser ManualWebsite
SnpEffGenomic annotation of SNP variantsOur GuideUser ManualWebsite
SRA toolkitWorking with NCBI's compressed SRA filesOur GuideUser ManualWebsite
TopHatMap and align NGS reads from RNAOur GuideUser ManualWebsite
UCSC binariesSet of tools for genomics dataOur GuideUser ManualWebsite
VCFtoolsTools for VCF filesOur GuideUser ManualWebsite