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openBIS: a flexible framework for managing and analyzing complex data in biology research.

Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B - BMC Bioinformatics (2011)

Bottom Line: Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.This framework can be extended and has been customized for different data types acquired by a range of technologies. openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies.The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland.

ABSTRACT

Background: Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.

Results: We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.

Conclusions: openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.

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Work and data flow of openBIS for Next Generation Sequencing. Integration of openBIS in the workflow of a Next Generation Sequencing core facility. Users can access openBIS through the openBIS webclient to enter new samples, track sample state and to download result data. Facility personnel registers samples after delivery and use openBIS to organize the workflow and to add processing quality control and metadata to the corresponding samples. Sequencing data undergoes real time analysis and the processed data is stored and connected to the samples metadata. Users receive a notification once the sequence data is ready for download.
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Figure 4: Work and data flow of openBIS for Next Generation Sequencing. Integration of openBIS in the workflow of a Next Generation Sequencing core facility. Users can access openBIS through the openBIS webclient to enter new samples, track sample state and to download result data. Facility personnel registers samples after delivery and use openBIS to organize the workflow and to add processing quality control and metadata to the corresponding samples. Sequencing data undergoes real time analysis and the processed data is stored and connected to the samples metadata. Users receive a notification once the sequence data is ready for download.

Mentions: We customized the openBIS framework to provide the core facility with a sample submission and tracking system (Figure 4). Users can enter the sample metadata within the respective incoming data space of the corresponding research group. Once the biological sample arrives at the core facility a facility member moves it from the incoming data space to the effective data space, where the metadata are only editable by the core facility personnel. The current metadata sample submission form and the sequencing services are configured for Illumina sequencing. They can easily be adjusted to alternative sequencing platforms by defining new sets of property types or by using metadata annotation systems provided by the respective instruments. A tracking system provides an automated e-mail functionality establishing a communication link between the core facility and the researchers indicating the status of key steps in the experimental process, such as the completion of DNA library processing and the generation of quality control and sequencing datasets.


openBIS: a flexible framework for managing and analyzing complex data in biology research.

Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B - BMC Bioinformatics (2011)

Work and data flow of openBIS for Next Generation Sequencing. Integration of openBIS in the workflow of a Next Generation Sequencing core facility. Users can access openBIS through the openBIS webclient to enter new samples, track sample state and to download result data. Facility personnel registers samples after delivery and use openBIS to organize the workflow and to add processing quality control and metadata to the corresponding samples. Sequencing data undergoes real time analysis and the processed data is stored and connected to the samples metadata. Users receive a notification once the sequence data is ready for download.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3275639&req=5

Figure 4: Work and data flow of openBIS for Next Generation Sequencing. Integration of openBIS in the workflow of a Next Generation Sequencing core facility. Users can access openBIS through the openBIS webclient to enter new samples, track sample state and to download result data. Facility personnel registers samples after delivery and use openBIS to organize the workflow and to add processing quality control and metadata to the corresponding samples. Sequencing data undergoes real time analysis and the processed data is stored and connected to the samples metadata. Users receive a notification once the sequence data is ready for download.
Mentions: We customized the openBIS framework to provide the core facility with a sample submission and tracking system (Figure 4). Users can enter the sample metadata within the respective incoming data space of the corresponding research group. Once the biological sample arrives at the core facility a facility member moves it from the incoming data space to the effective data space, where the metadata are only editable by the core facility personnel. The current metadata sample submission form and the sequencing services are configured for Illumina sequencing. They can easily be adjusted to alternative sequencing platforms by defining new sets of property types or by using metadata annotation systems provided by the respective instruments. A tracking system provides an automated e-mail functionality establishing a communication link between the core facility and the researchers indicating the status of key steps in the experimental process, such as the completion of DNA library processing and the generation of quality control and sequencing datasets.

Bottom Line: Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.This framework can be extended and has been customized for different data types acquired by a range of technologies. openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies.The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland.

ABSTRACT

Background: Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.

Results: We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.

Conclusions: openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.

Show MeSH