July, 2013

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Conferences in 2014

20th International Mass Spectrometry Conference will take place in Geneva, Switzerland, August 24-29, 2014. Geneva was selected as host city of the 20th IMSC, which will be taking place at the Centre International de Conférences Genève (CICG).


The 5th Conference on Systems Biology of Mammalian Cells (SBMC) 2014 will be held in Germany in July 2014.

Data sharing and management – web solution

Metadata central storage

The central data storage will be realized as combination of local data storage (located on the institution) for raw data and one central data storage selected meta-data. Central data storage will be based on distributed relation ORACLE database to deal with the amount and structure of the meta-data. The data structures in central database will be defined generally to cover all the different meta-data types and to upgrade the structures in the future.

Data availability

The central data storage will serve as the first option for searching the experimental data through meta-data and allow the user to find the proper experiment and results. All the meta-data will be available using the XLM data structures exchange.
The solution based on relational database allows:
– standard access to the metadata using SQL standard language and support of wide range of database interfaces
– high accessibility of the system will be allowed by distribution to more computers using GRID technology of CLUSTERING
– fast information search – the usage of data structures indexing and advanced algorithms of query execution plans will minimize the time response of the data storage
– standardized system control – the commercial database ensure the safe and secured operation of the database

Information system of central data storage:

The central database will be in cooperation with the information system. The information system will provide the parameterization of the central storage, user accounts control and policy. The data from central database will be presented using the web presentations to the different kind of the scientific and laic public controlled by the access rights.

Central storage interface:

The interface will be used as an interpreter between central data storage, local data storage and visualization framework.

Visualization framework:

The user friendliness of the central database will be supported by the visualization framework. The visualization framework will be implemented as several software modules and interface for extension of information system. The visualization framework will allow simple and intelligible visualization and comparison of the meta-data and result of searches. It will be based on the mix of existing modules and third party modules. The third party modules could be plugged into the central data storage for the user of the system. The modules will be focused on raw data processing and data mining and aggregation of the meta-data. Standard interface of the central data storage will allow the user to upload the mined information back into the central storage, describe it and integrate it into current structures.

One part of the web solution will be the offer of tools for raw data post-processing. These tools will be highly specialized tools for experimental data processing. The tools can be used by anyone to produce the metadata from raw experimental data and share the metadata using BioWes web solution. The list of the tools can be extended by any third party tool for biological data processing. Several tools will be developed directly under the project:

– Cell time lapse image processing and representation
– LC-MS measurements filtration and analysis
– Software for behavior analysis of aquatic organisms

Local data management tools

The main purpose of local data management tool is to organize and store the raw experimental data directly on the site of the institution (experimenter). The local data management tool will provide the functionality of data storing, searching, filtration and reporting. The tool will be connected to the Protocol generator to support the reporting of experiments on the higher level of metadata. Local data management will be realized as a specialized database that will be optimized to the type of experimental data produced by particular institution. The database with uniform interface will be modified according to the needs of the particular experimenter to reach the aims of different experiments.

The local management tool will provide the communication module (interface) to global data management tool (web based data sharing). The global data management tool will be used for meta-data sharing between different institutions and the public. The process of communication between local and global data management tools will be under full control of the institution. Therefore only the meta-data can be shared with the rest of scientific community or the public. The advantage of this approach is the direct control of „what I am sharing with the others“.

There are many different solutions and technologies for raw data storage among the institutions. The review of technologies will be realized during the first year of the project to select the best technology for local data management tool.

The Open Biological and Biomedical Ontologies

Ascomycete phenotype ontology was added into OBO CVS repository.


The ontology serve as a structured controlled vocabulary for the phenotypes of Ascomycete fungi. The ontology is related to the Saccharomyces genome database. You can find more details about the database here: http://www.yeastgenome.org/

Pilot of protocol designer

The discussion with partners involved in the testing of the BioWes system identified the bottle necks of the developing solution. The definition of the electronic template of the protocol was the main issue. The XML language was originally used for the definition of the protocol template. This way of definition is very beneficial from standardization point of view but it is not very user friendly. Therefore the WYSIWYG (graphical user interface) editor Protocol designer has been developed to solve this issue. Using the Protocol designer, every technician can prepare the protocol template and use it for description of experiments.


New ontology focused on the fish production was developed in the frame of Aquaexcel projects (http://www.aquaexcel.eu)

The goal of the AQUAEXCEL-ATOL ontology is to define and organize livestock traits, with a focus on the main types of fish production (meat, feed and fertility) in accordance with societal priorities (animal welfare, product quality, etc.).

This ontology will be a reference for semantic search tools in order to improve queries on bibliographic resources about livestock animal phenotypes. Making homogeneous database annotation, it opens the possibility for meta-analysis and modeling.

Follow the link to access the ontology tool:


A tutorial on the tool can be found at:


Protocol generator testing

BioWes testing at the Core Facility Cell Imaging and Ultrastructure Research of University of Vienna.

The prototype of the Protocol generator and the Local database was installed in the Cell physiology and scientific film laboratory of Core Facility Cell Imaging and Ultrastructure Research of University of Vienna. The laboratory seeks the way how to contribute to the understanding of the organization and dynamics of plant cells under various physiological and ecological conditions. The laboratory will use the system of electronic protocols for description of the advanced video light and electron microscopy combined with fluorescence techniques.