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 was used by the evaluation team, in their laboratory at TU Delft, to document, execute and analyze microbial cultivation in shake flasks, batch bioreactors and chemostat bioreactors.

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 was used by the evaluation team, in their laboratory at TU Delft, to document, execute and analyze microbial cultivation in shake flasks, batch bioreactors and chemostat bioreactors.

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 was used by the evaluation team, in their laboratory at TU Delft, to document, execute and analyze microbial cultivation in shake flasks, batch bioreactors and chemostat bioreactors.

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: The Riffyn SDE is a cloud-based software-as-a-service architecture hosted and operated by Riffyn in both multi-tenant and single-organization configurations on Amazon Web Services.

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 is a cloud-based software-as-a-service architecture hosted and operated by Riffyn in both multi-tenant and single-organization configurations on Amazon Web Services.

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 is a cloud-based software-as-a-service architecture hosted and operated by Riffyn in both multi-tenant and single-organization configurations on Amazon Web Services.

Techniques: Derivative Assay

Journal: Clinical and Translational Allergy

Article Title: Secretory protein beta‐lactoglobulin in cattle stable dust may contribute to the allergy‐protective farm effect

doi: 10.1002/clt2.12125

Figure Lengend Snippet: BLG and endotoxin levels in stable dust and ambient air of cattle farms. (A) BLG in dust of cattle stables, which was collected by different methods, detected in immunoblot: stable dust extract SDE1 (Table , set 1, Vet) = dust wiped from elevated surfaces; SDE2 (Table , Set 1, Bav) = dust deposition on cardboard box over 3 weeks; SDE3 (Table , set 3, Vet) = dust collected by air filtering (1 representative example of at least 3 repetitions per collection method is shown; due to time interval between examination, strips of different individual blots are shown). ( B ) Stable dust extracts (SDE), all collected by wiping, from cattle farms ( n = 14; Table , set 2, C1–14) and poultry stable ( n = 8; Table , set 2, P1‐8) investigated by BLG‐specific ELISA (mean +/‐ SD; representative of 3 repetitions). ( C ) BLG in stable dust (sample SDE 2) confirmed by MS/MS‐LC in SDE separated via SDS‐PAGE, stained by Roti‐Blue® and the major band around 18 kDa excised. ( D ) Protein of the excised band in MS/MS‐LC (proteins UniProtKB P02754 and B5B0D4 with difference of 2 amino acids in sequence). ( E ) BLG‐concentration in air samples at different distances from cattle stable (Table , set 4, n = 4 filter/distance), extrapolated to the human respiratory volume per 24 h, determined in ELISA (1 m = outside the stable in front of open window; 156 m and 290 m distance from cattle stable, sampled on cellulose filters; at the mountain site Sonnblick at 3106 m above sea level, sampled on quartz fiber filters); and ( F ) in immunoblot with bovine BLG‐specific antibodies (1 = 1 m, 2 = 156 m, 3 = 290 m, Co = empty control filter; 3 different time points from E shown). ( G ) Levels of endotoxin were determined in dust samples of cattle ( n = 14) and poultry stable ( n = 8) (Table , set 2) by LAL test, and ( H ) in dust samples collected in different distances to cattle stable. ( I ) Occurrence of BLG in different households (hh). BLG in sieved bed dust samples from beds of cattle farm households (Cattle hh. N = 14) , poultry farm households (Poultry hh, n = 8) or urban apartments (Urban hh, n = 10), detected by an anti‐BLG antibody in ELISA (mean of 2 repetitions). BLG (commercial beta‐lactoglobulin) = positive control; OVA (ovalbumin) and Co (empty control paper filter) = negative control. M: protein weight marker in kDa. Arrows indicate monomeric (around 18 kDa) and dimeric (38 kDa) BLG. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001

Article Snippet: Endotoxin levels in dust samples from different distances as well as aliquots of SDE+ and SDE‐ were measured by LAL (Limulus Amoebocyte Lysate) assay (Kinetic‐QCLTM Kinetic Chromogenic LAL Assay, 50–650U, LONZA, Switzerland) in the ISO17025‐accredited testing laboratory at the unit Water Hygiene, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Austria.

Techniques: Western Blot, Enzyme-linked Immunosorbent Assay, Tandem Mass Spectroscopy, SDS Page, Staining, Sequencing, Concentration Assay, Control, Positive Control, Negative Control, Marker