Workflows

Widgets

There is a huge quantity of information generated in Life Sciences, and it is dispersed in many databases and repositories. Despite the broad availability of the information, there is a great demand for methods that are able to look for, gather and display distributed data in a standardized and friendly way.

CARGO has been designed to provide pieces of minimal, relevant and descriptive biological information, and be used by experimental biologists with no training in bioinformatics. A mini-application of CARGO is embedded below to facilitate, integrate and visualize results from Internet resources, independently of their native format or access method. CARGO uses small agents, called widgets, which are supported by a Rich Internet Application (RIA) paradigm based on AJAX.

To get you started first select a widget (i.e iHOP), type the Ensemble example for Breast cancer type 1 susceptibility protein (RING finger protein 53) ENSG00000012048 and then click “Run”.

	Cargo
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Specialised Systems

These are in-house tools that have been developed by INB research groups and pointers are available following this link: Special Systems

MOWServ

The main goal of this interface is to allow an integrated INB web services, allowing the exploration and alm of the generated data.

Jorca

User oriented software emerged on the ESP-SOL project and extended and generalized in the INB to facilitate integration and engage the use of INB webservices

mAPI

The huge growth of internet has supposed the raise of a huge number of formats, data and services that are partically developed on parallel and are incompatible among them. We have developed a new framework for the develpement of applicatoins with the main characteristic of be modular and adaptable to different scenarios. The natural flexiblity of the framework allows the conecction to different data sources and combine their contents for showing all to the user with a easy to use and powerful interface.

MOWServ Workflow List

Access to the list of workflows enacted by MOWServ

aGEM

The “anatomic Gene Expresssion Mapping (aGEM)” Platform is a development conceived to integrate phenotypic information from spatial and temporal distribution of expressed genes in whole organisms. The aGEM Platform has been built extending the Distributed Annotation System (DAS) protocol that was originally designed to share genome annotations over the WWW. The aGEM Platform provides information to answer three main questions (1) Which are the genes that are expressed in a given anatomical component?, (2) in which anatomical structures a given gene (or set of genes) is expressed?, and (3) is there any correlation among these findings?. Currently this platform includes several well-known mouse resources (EMAGE, GXD and GENSAT), hosting gene expression data obtained mostly from in situ techniques together with a broad set of image derived annotations.

Flexibility web

The aim of this web tool is help the researcher in the study of protein flexibility questions. The proteins that are suitable for studying are all valid proteins fragments, this means fragments with no gaps in their sequence with valid distances between atoms.

The methods used to study the proteins only work with the alpha carbons of the protein. The protein input is briefly simulted to get a trajectory, and his trajectory is analyzed to get the associated eigenvectors and eigenvalues, allowing to reconstruct the trajectory and perform the various analysis on this data.

The simulations (and the corresponding eigenvectors and eigenvalues) can be obtained in different ways, mainly:

• Normal Mode Analysis
• Discrete Molecular Dynamics
• Brownian Dynamics