Service

Molecular Biology and Bioinformatics

The Molecular Biology and Bioinformatics facility applies molecular biology techniques that analyse 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 person responsible for the service is in charge of providing the training and he/she will be also in charge of the supervision 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. The platform also provides advice about the design of Data Management Plans that follow the FAIR principles as requested by EU and Spanish projects.

Technical resources and equipment

The equipment of the Molecular Biology service includes:

  • Four PCR machines
  • Electrophoresis systems
  • PFGE gel system (CHEF DR-II, Biorad)
  • Gel doc equipment provided with the analysis software (iBright CL 1500, Invitrogen)
  • Real-Time PCR machine (Cfx, Biorad)
  • Biomolecules analyzer (QSep100, Bio Optic)
  • Fluorometer (Qubit Q32857, Invitrogen) and Spectrophotometer UV-Vis (NanoDrop One,Thermo Scientific) for qualify and quantify nucleic acids and proteins
  • In addition, the 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:

  • High Performance Computing cluster. One master/login node (Fujitsu Primergy RX2530 M2 server) and 22 high performance computing nodes with a total of 396 physical cores and 4.6 T of RAM (10 x Supermicro, 12 x IBM iDataPlex). It has 830 T of storage in a shared parallel distributed filesystem.
  • 3 DELL workstations: DELL PowerEdge T710 servers with 2 x 4-core Intel Xeon E5620 processors, 16-60G of RAM and 1 x 2T hard drive..

LINK TO MARBITS BIOINFORMATICS PLATFORM