Molecular Biology and Bioinformatics

The Molecular Biology and Bioinformatics facility allows the application of molecular biology techniques based on the analysis of the DNA and/or RNA content, nucleotide sequence and epigenetic modifications of marine organisms, to unravel their identity, activity and their roles in the marine ecosystem, as well as the function of their genes in key biological processes. This service gives support and training to students and researchers of the ICM or external visitors who wish to use some of these techniques applied to their samples. The operation is based on self-service. The responsible of the service is in charge of providing the training and it will be also in charge of giving control and technical support during processing.

In terms of bioinformatics, the facility allows users to analyze omics data (metagenomics, metatranscriptomics, metabarcoding, etc.) in a High-Performance computing cluster. Depending on their needs, users are given storage, computation and RAM usage quotas. The previous parameters are monitored to register the usage that they make of the infrastructure, which is billed on a regular basis. The service manages users, groups of users and their associated permissions and installs and manages third-party software and biological databases. Additionally, a backup for user's data is provided, even though the user is still responsible for keeping an ex-situ backup copy. The platform may also manage or supervise big-data transmission from their source to the computer cluster, check for their integrity and store them. Upon request, the platform advice users on general analysis of DNA/RNA extraction and sequencing data, bisulfite conversion, library preparation, quality check and sequence cleaning, assembly and annotation of genomes and metagenomes, and analyses of microbial diversity of environmental samples among others. The platform advice users on how to upload and store data in public repositories, such as ENA or NCBI. The platform offers users a basic formation in UNIX computing environments, as well as on several applications on computational biology. It also develops small pieces of custom software and bioinformatics pipelines.

Technical resources and equipment

The equipment of the Molecular Biology service includes three PCR machines, electrophoresis systems, DGGE and PFGE gels systems, Chemidoc XRS equipment and Quantity One software, D-Code system, Qubit Fluorometer, Nanodrop ND-1000 spectrophotometer. Further facilities include general equipment needed for the development of the different protocols, such as centrifuges, hybridization oven, heating bath, thermal incubator, desiccator with vacuum pump, laminar flow hoods, microwave, vortex and a heating mixing plate.

The equipment for Bioinfomatics analysis consists of: Master/login node: The master/login node is called marbits. It’s Fujitsu Primergy RX2530 M2 server with 2 x Intel Xeon E5-2603v4, 2 x 240 GB SSD disks and 64GB RAM. It runs CentOS 7.4, a RedHat-based linux distribution, with OpenHPC on top and slurm as job scheduler. High-performance computing nodes: The 22 computing nodes are divided in 3 classes according to their configuration and brand: Storage: General data storage is managed by a parallel filesystem (Lustre) shared by other resources from the CMIMA, with 620TB of disk space. Network: All computing nodes are connected via a 1 Gbps SMC Networks SMC8150L2 switch with 50 x 10/100/1000BASE-T ports. Communication with the Lustre filesystem is provided by a 10 Gbps Netgear XS748T switch. DELL workstations: Several applications needing X-window forwarding can be carried out in the DELL workstations. These are 3 DELL PowerEdge T710 servers with 2 x 4-core Intel Xeon E5620 processors, 16-60G of RAM and 1 x 2T hard drive.