Journal: Scientific Data

Article Title: Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

doi: 10.1038/sdata.2018.195

Figure Lengend Snippet: ( a ) All data on each experiment in the Riffyn SDE is extracted and flattened into a statistical data-frame compatible with nearly any modern analysis software (including R, JMP, SAS, Tableau, Minitab, etc.). This data-frame is composed of all variables defined on a Riffyn SDE process or experiment, including sample identifiers, parameter settings, start/stop times, dates, measurement data and units. The variables are presented as columns in the data-frame and grouped by step in the process. Multiple experiments executed on that same process (regardless of version) are stacked together such that data are aligned into common columns. If versions of a process diverge, gaps are left in the table where such variables are missing in the process. ( b ) Individual process data tables can be further combined into a “Master Process” data table composed of all data from all linked processes used in performing an experiment, including material preparation, equipment set-up, fermentation, and analytical chemistry processes. Data from these processes are joined together using the material flow graph defined by the Master Process in the Riffyn SDE, and the material identifiers automatically tracked by the Riffyn SDE.

Article Snippet: The Riffyn SDE software automatically tracks changes to protocols and allows generation of a new version at any time.

Techniques: Software

Journal: Scientific Data

Article Title: Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

doi: 10.1038/sdata.2018.195

Figure Lengend Snippet: Data is entered into Riffyn via parsing of instrument files, querying of a database, or via manual data entry. All data is passed through a firewall and contextualized based on the Riffyn SDE process design. Any files parsed during the data upload are additionally stored in their native format. All contextualized data is exported as a flat csv file with all data, material information, and setpoints captured. This flat file is built with each variable as a column, and each row as an observation. Multiple tables are concatenated together across each version of the process to provide a comprehensive, cross-version table that captures all data across the development of the process.

Article Snippet: The Riffyn SDE software automatically tracks changes to protocols and allows generation of a new version at any time.

Techniques:

Journal: Scientific Data

Article Title: Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

doi: 10.1038/sdata.2018.195

Figure Lengend Snippet: ( a ) The ad hoc manual method typically used by experimenters requires visual inspection of the growth curves to exclude data points believed to be outside of exponential phase. After exclusion of such points, growth rates are calculated by regression of the remaining data points. This approach is subject to subjective interpretation and human bias. ( b ) The automatic growth rate calculation method implemented in scripts associated with the cultivation processes in the Riffyn SDE. An algorithm, rather than visual inspection, is used to identify values outside the exponential growth phase. Growth rates are then calculated using the remaining data points. Physiological parameters derived from such growth rates are objectively calculated, without human bias.

Article Snippet: The Riffyn SDE software automatically tracks changes to protocols and allows generation of a new version at any time.

Techniques: Derivative Assay

Journal: Scientific Data

Article Title: Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

doi: 10.1038/sdata.2018.195

Figure Lengend Snippet: ( a ) All data on each experiment in the Riffyn SDE is extracted and flattened into a statistical data-frame compatible with nearly any modern analysis software (including R, JMP, SAS, Tableau, Minitab, etc.). This data-frame is composed of all variables defined on a Riffyn SDE process or experiment, including sample identifiers, parameter settings, start/stop times, dates, measurement data and units. The variables are presented as columns in the data-frame and grouped by step in the process. Multiple experiments executed on that same process (regardless of version) are stacked together such that data are aligned into common columns. If versions of a process diverge, gaps are left in the table where such variables are missing in the process. ( b ) Individual process data tables can be further combined into a “Master Process” data table composed of all data from all linked processes used in performing an experiment, including material preparation, equipment set-up, fermentation, and analytical chemistry processes. Data from these processes are joined together using the material flow graph defined by the Master Process in the Riffyn SDE, and the material identifiers automatically tracked by the Riffyn SDE.

Article Snippet: To evaluate the ability of the Riffyn SDE software to capture and communicate complex protocols, record diverse data types, and enable data analysis, sharing, and reusability, we applied it to a study to quantify the aerobic growth characteristics of the industrially relevant yeast Ogataea polymorpha ( syn.

Techniques: Software

Journal: Scientific Data

Article Title: Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

doi: 10.1038/sdata.2018.195

Figure Lengend Snippet: Data is entered into Riffyn via parsing of instrument files, querying of a database, or via manual data entry. All data is passed through a firewall and contextualized based on the Riffyn SDE process design. Any files parsed during the data upload are additionally stored in their native format. All contextualized data is exported as a flat csv file with all data, material information, and setpoints captured. This flat file is built with each variable as a column, and each row as an observation. Multiple tables are concatenated together across each version of the process to provide a comprehensive, cross-version table that captures all data across the development of the process.

Article Snippet: To evaluate the ability of the Riffyn SDE software to capture and communicate complex protocols, record diverse data types, and enable data analysis, sharing, and reusability, we applied it to a study to quantify the aerobic growth characteristics of the industrially relevant yeast Ogataea polymorpha ( syn.

Techniques:

Journal: Scientific Data

Article Title: Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

doi: 10.1038/sdata.2018.195

Figure Lengend Snippet: ( a ) The ad hoc manual method typically used by experimenters requires visual inspection of the growth curves to exclude data points believed to be outside of exponential phase. After exclusion of such points, growth rates are calculated by regression of the remaining data points. This approach is subject to subjective interpretation and human bias. ( b ) The automatic growth rate calculation method implemented in scripts associated with the cultivation processes in the Riffyn SDE. An algorithm, rather than visual inspection, is used to identify values outside the exponential growth phase. Growth rates are then calculated using the remaining data points. Physiological parameters derived from such growth rates are objectively calculated, without human bias.

Article Snippet: To evaluate the ability of the Riffyn SDE software to capture and communicate complex protocols, record diverse data types, and enable data analysis, sharing, and reusability, we applied it to a study to quantify the aerobic growth characteristics of the industrially relevant yeast Ogataea polymorpha ( syn.

Techniques: Derivative Assay