In order to monitor, describe and understand the marine environment, many research institutions are involved in the acquisition and distribution of ocean data, both from observations and models. Scientists from these institutions are spending too much time looking for, accessing, and reformatting data: they need better tools and procedures to make the science they do more efficient. The U.S. Integrated Ocean Observing System (US-IOOS) is working on making large amounts of distributed data usable in an easy and efficient way. It is essentially a network of scientists, technicians and technologies designed to acquire, collect and disseminate observational and modelled data resulting from coastal and oceanic marine regions investigations to researchers, stakeholders and policy makers. In order to be successful, this effort requires standard data protocols, web services and standards-based tools. Starting from the US-IOOS approach, which is being adopted throughout much of the oceanographic and meteorological sectors, we describe here the CNR-ISMAR Venice experience in the direction of setting up a national Italian IOOS framework using the THREDDS (THematic Real-time Environmental Distributed Data Services) Data Server (TDS), a middleware designed to fill the gap between data providers and data users. The TDS provides services that allow data users to find the data sets pertaining to their scientific needs, to access, to visualize and to use them in an easy way, without downloading files to the local workspace. In order to achieve this, it is necessary that the data providers make their data available in a standard form that the TDS understands, and with sufficient metadata to allow the data to be read and searched in a standard way. The core idea is then to utilize a Common Data Model (CDM), a unified conceptual model that describes different datatypes within each dataset. More specifically, Unidata (<a href="http://www.unidata.ucar.edu" target="_blank">www.unidata.ucar.edu</a>) has developed CDM specifications for many of the different kinds of data used by the scientific community, such as grids, profiles, time series, swath data. These datatypes are aligned the NetCDF Climate and Forecast (CF) Metadata Conventions and with Climate Science Modelling Language (CSML); CF-compliant NetCDF files and GRIB files can be read directly with no modification, while non compliant files can be modified to meet appropriate metadata requirements. Once standardized in the CDM, the TDS makes datasets available through a series of web services such as OPeNDAP or Open Geospatial Consortium Web Coverage Service (WCS), allowing the data users to easily obtain small subsets from large datasets, and to quickly visualize their content by using tools such as GODIVA2 or Integrated Data Viewer (IDV). In addition, an ISO metadata service is available through the TDS that can be harvested by catalogue broker services (e.g. GI-cat) to enable distributed search across federated data servers. Example of TDS datasets can be accessed at the CNR-ISMAR Venice site <a href="http://tds.ve.ismar.cnr.it:8080/thredds/catalog.html" target="_blank">http://tds.ve.ismar.cnr.it:8080/thredds/catalog.html</a>.
MUREN: a robust and multi-reference approach of RNA-seq transcript normalization