Project: Bridging Integrative OMICS and Structures for Community Applications Production and Exchange
The sequencing of the human genome in 2000 has been the catalyst of tremendous scientific and technological breakthroughs and heterogeneous Big Data. Those advances challenge our understanding of Biology and Human Health and require new perspectives and highly integrated software to handle, query and visualize biological data in the easiest yet most relevant way._x000D__x000D_Among those breakthroughs, the number of molecular 3D structures has been multiplied 10-fold in the last 10 years, offering a coverage of 25% of the human proteome (70% with modeling strategies) compared to approximately 1% 10 years ago. This drastic increase in the 3D coverage of the human proteome challenges our understanding and perspectives on molecular interactions, kinetics and recognitions at Systems level such as pathways and cellular networks. It also created major issues in the understanding and exploration of the structural aspects of Biology: in fact many proteins are represented by dozens if not hundreds of structures to the point where even specialists are having difficulties to extract the structural information relevant to their study. To be used efficiently and to be integrated as qualitative and quantitative data in System and Network Biology, the study of molecular structures must shift from the “static” analysis of a single structure to the integrated analysis of these protein’s structure snapshots, allowing to better capture and comprehend the dynamic nature of molecules, interactions and networks._x000D__x000D_With specialists of biological sequences (CALIPHO, GeneBio) and structures (CSB, IGBMC, BIONEXT) who have already worked together in European projects, we propose to develop a Unique Structure Model (USM) to give a unique access to relevant structural knowledge for each protein, by integrating experimental structures from the PDB and homology models in a single data representation. Applications will concern biologists, chemists and pharmaceutics and ease the use and integration of structural data both for illustrative purposes and as an important source of quantitative and qualitative data. Structural models corresponding to isoforms and SNP variants will be handled by the automated homology modeling expert system SWISS MODEL. All the complexity and rich data will be treated by fast and validated integrative approaches in order to present the user only the relevant information. As an example, the approach will give an easy access to the distinct conformational states of a protein, to its distinct isoforms and modified forms (PTM), will link SNPs to genetic diseases and also provide details about the known and predicted binding sites and Ps. This information will be stored in a database and easily accessed thanks to a secured API. By hiding the unnecessary complexity of structural data while still allowing an easy yet relevant access to structural knowledge, the BioScape project will enable the effective merge of Integrative Structural Biology with System and Network Biology. As a powerful demonstrator, USM will be fully integrated to the BIONEXT 3D Molecular Viewer BioViz, to democratize the use and exploration of knowledge on structures without any prior expertise in Structural Biology._x000D__x000D_In a second phase of the BioScape project, the USM will be used to power an innovative tool (BioNote) to create, visualize, modify and exchange informative, realistic and interactive molecular animations (called structural annotations). BioNote graphical interfaces will be inspired by movies edition software such as Adobe Premiere, allowing for the easy creation of structural annotations by the dragging & dropping of animation events on a timeline. _x000D__x000D_To valorize BioViz and BioNote and create a novel innovative channel for publishing scientific discoveries and technological innovations, members of BioScape will create a Network of Scientific Reference Databases (NSRD) starting with 6 core databases, representing hundreds of thousand users. The structural annotations will be easily exchanged throughout the NSRD network thanks to standardized formats and the creation of a Structural Annotation Ontology that will be proposed to the OBO consortium to describe and classify molecular animations illustrating biological objects, mechanisms and properties. _x000D__x000D_Additionally, the exceptional access to potential users and clients provided by the NSRD network will help consolidate the leadership positions of both BIONEXT and GeneBio. In particular, we will benefit from this situation by creating a second and novel channel of publication (software), namely a Biological Appstore & Services (BAS) inspired by Apple's Appstore and Google Play. Private and public organizations will be given the opportunity to easily create, share and sell their own solutions (offline applications and SaaS), thus reducing the time and cost to market of innovative solutions and helping private companies to keep up with the worldwide high-rate of innovations. _x000D_
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Acronym
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BioScape
(Reference Number: 8314)
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Duration
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15/10/2013 - 15/05/2016
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Project Topic
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BioScape unites experts of sequence, annotation and structure to provide 3 solutions: a) a Unique Structure Model to reduce the structural complexity for System and Network Biology; b) easily create, modify and exchange interactive realistic molecular movies; c) a Biological Appstore & Services
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Network
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Eurostars
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Call
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Eurostars Cut-Off 10
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Project partner
