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Creator: Daniel Seaton
Submitter: Daniel Seaton
Creator: Daniel Seaton
Submitter: Daniel Seaton
Creator: Daniel Seaton
Submitter: Daniel Seaton
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
The calculation of amino acid uptake rates for cells of Sulfolobus solfataricus P2 grown on caseinhydrolysate was performed based on the relative consumption of individual amino acids from the growth medium and the previously published absolute concentration of amino acids in the used growth medium.
Creator: Helge Stark
Submitter: Helge Stark
qATP values were calculated based on fermentation product formation and expected used biochemical pathways. These were averaged and used for calculation of the ATP required for maintenance and for growth. These data were subsequently used to calculate the qATP at the maximal growth rate by extrapolation
Creator: Martijn Bekker
Submitter: Martijn Bekker
- Calculations of predictions of all identified proteins of P. cordatum
- Calculations of fold-changes of all identified proteins (cell vs. nuclei fraction) of P. cordatum
- Calculations of predictions of proteins of unknown function of_ P. cordatum_
- Calculations of fold-changes of unknowns (cell vs. nuclei fraction) of P. cordatum
Tab color: all identified proteins, purple; unkowns, green
Creators: None
Submitter: Jana Kalvelage
14CO2 assimilation in the night-time, in plants of Col, prr7prr9; Ws, lhycca1 genotypes at 18 and 28 days, and partitioning among cellular fractions.
Creator: Gavin George, Samuel Zeeman
Submitter: Andrew Millar
It is a description of the maternal clinical data, fetal Doppler ultrasound data and delivery data of both groups of cases (late-onset fetal growth restriction) and controls (normal growth).
Creator: Gabriela Loscalzo
Submitter: Gabriela Loscalzo
It is a description of the maternal clinical data, fetal Doppler ultrasound data and delivery data of both groups of cases (late-onset fetal growth restriction) and controls (normal growth).
Creator: Gabriela Loscalzo
Submitter: Gabriela Loscalzo
Creator: Joerg Stuelke
Submitter: Leif Steil
Table describing the catabolite repression of β-xylosidase by different carbon sources(glucose, sorbitol, fructose, maltose, glycerol. mannitol) in various mutants of CcpA cofactors (HprK, crh)
Creator: Joerg Stuelke
Submitter: Leif Steil
The file contains an UMAP representation illustrating the expression of the stem cell marker Cd34 in all identified cell clusters.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Jurgen Haanstra
Submitter: Jurgen Haanstra
Cell volume_trk_
Creator: Silvia Petrezselyova
Submitter: The JERM Harvester
Cellular size and granularity (measured by FACS) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Batch sample publishing
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, and additional Mn2+ (0.15 mM) added.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, without NAD recycling, but with additional Mn2+ (0.15 mM) added.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, but without additional Mn2+ added.
Creators: Jacky Snoep, Lu Shen
Submitter: Jacky Snoep
S. pyogenes was grown in C-limited cultures at pH 6.5 and 7.5 and at a growth rate of 0.05 The glnA mutant strain shows decreased growth in low glutamine and excess glutamate conditions and no growth at all in low glutamine and low glutamate conditions. Preliminary results of glucose-limited chemostat cultures indicate a reversion of the pH dependency of the shift from homolactic to more mixed acid fermentation: wild type - lactate/formate ratio at pH 6.5 = 11.8, at pH 7.5 = 2.8 glnA mutant - ...
Creators: Antje Sieg, Silvio Hering, Martijn Bekker
Submitter: Antje Sieg
E. faecalis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15
Creators: Ibrahim Mehmeti, Maria Jonsson
Submitter: Martijn Bekker
L. lactis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05, 0.15 and 0.40
Creator: Martijn Bekker
Submitter: Martijn Bekker
S. pyogenes was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15
Creators: Martijn Bekker, Tomas Fiedler
Submitter: Martijn Bekker
Measurements on Km, Vmax and allosteric activation or inhibition of the main L-lactate dehydrogenase
Creator: Tomas Fiedler
Submitter: Martijn Bekker
Creators: Xiaokang Zhang, Marta Eide, Odd André Karlsen, Inge Jonassen, Anders Goksøyr, Jared V. Goldstone; John Stegeman
Submitter: Xiaokang Zhang
Creators: Xiaokang Zhang, Marta Eide, Odd André Karlsen, Inge Jonassen, Anders Goksøyr, Jared V. Goldstone; John Stegeman
Submitter: Xiaokang Zhang
acetic acid puls during acidogenesis shift to solventogensis back-shift to acidogenesis butyric acid puls during acidogenesis
Creator: Sebastian Curth
Submitter: Sebastian Curth
butyric acid pulse during acidogenesis acetic acid pulse during acidogenesis butyric acid pulse during solventogenesis
Creator: Sebastian Curth
Submitter: Sebastian Curth
This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR and BED files. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
GEO format data
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Contains CML dictionaries created to store deep eutectic solvent data with CML.
Contains CML created for experimental, simulation and predicted data. Predictions were made based on experimental data using a gradient boosting decision tree.
Creators: Gudrun Gygli, Xinmeng Xu, Juergen Pleiss
Submitters: Gudrun Gygli, Xinmeng Xu
Creators: None
Submitter: Sarah Kirstein
Archive contains python scripts for image analysis
Creators: Malte Herold, Antoine Buetti-Dinh
Submitter: Malte Herold
Figure 5D
Creator: Yin Hoon Chew
Submitter: Andrew Millar
Combined taxonomy table of abundance of OTUs (Operational Taxonomy Units) in both freshwater and saltwater samples from 16S V3-V4 Illumina sequencing of gut microbiota. Primers used for sequencing are given in https://fairdomhub.org/sops/270 The OTUs are presented in number of counts per sample (n=349). Each row represent one sample. Raw data are available in the Sequence Read Archive database under accession number SRP119730 (https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP119730).
Creators: Inga Leena Angell, Lars Snipen, Jon Olav Vik
Submitter: Inga Leena Angell
RNAseq data file, source: /mnt/users/fabig/DigiSal/crispr_RNAseq/samples_ELOVL2/final/2018-06-25_samples_ELOVL2/combined.counts
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
Tail intensities (%) measured by the Comet Assay as indication of DNA fragmentation in blood cells of Atlantic cod exposed to PAHs and PFASs
Creator: Karina Dale
Submitter: Karina Dale
Photos of drop test conpresed in .zip file
Creator: Jaromir Zahrádka
Submitter: The JERM Harvester
nha1, ena1-5, double deletion
Creator: Jaromir Zahrádka
Submitter: The JERM Harvester
The output includes the similarity matrix of LDH enzymes based on comparison of the electrostatic potentials at allosteric and catalytic binding sites, separately. The similarity indices were generated by the PIPSA program (http://projects.villa-bosch.de/mcmsoft/pipsa/3.0/).
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Comparison of Kcat values model and values from literature. Model values are based on Vmax enzyme parameters (maximum activity per enzyme molecule). Literature values are largely based on whole cell enzyme extract assays and do not take into account allosteric control. In addition activity is measured at varying time points and varying conditions. The error based on differences in enzyme concentrations at different time points and the error in protein copy number measurements is taken into account ...
Creator: Niels Zondervan
Submitter: Niels Zondervan
L. lactis was grown in rich THY medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.
Creator: Martijn Bekker
Submitter: Martijn Bekker
Comparison of model SS metabolite concentrations with measured values using 1000x sampling from the Gausian distribution of the measured values based on multiple replicates per measured conditions. Graphs showing the distribution of measured and simulated metabolite concentration for 95 mutand (KO, OE), perturbation and time series measurements. Model simulations performed using 24h proteomics with modification of enzyme parameters for KO and OE mutants.
Creator: Niels Zondervan
Submitter: Niels Zondervan
Analysis of the sequences of PGM1 from several Synechocystis strains revealed a different annotation for Synechocystis sp. PCC 6803, which included a 16-amino acid N-terminal extension that is missing in the other strains. Additionally, the experimentally validated transcriptional start site from Synechocystis sp. PCC 6803 suggests a shorter open reading frame for PGM1, with Met 17 as putative translational start site. To clarify if the N-terminal extension is an annotation error, we prepared ...
Creator: Sofia Doello
Submitter: Sofia Doello
Culture conditions along with substrate and product compositions throughout the culture.
Creator: Alejandro Martínez Rey
Submitter: Alejandro Martínez Rey
Creator: Antoine Buetti-Dinh
Submitter: Antoine Buetti-Dinh
Creators: None
Submitter: Marta Eide
Creators: None
Submitter: Marta Eide
Creators: None
Submitter: Marta Eide
Creators: None
Submitter: Marta Eide
Creators: None
Submitter: Marta Eide
Concentrations of 22 extracellular metabolites (major medium components) from T. b. brucei 427
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Table with InterPro annotations, matches to Pcitri.v1 genome and differential expression between mated and virgin P.citri females for the transcripts in the consolidated P. citri transcriptome.
Creator: Mojca Juteršek
Submitter: Mojca Juteršek
Transcriptome sequences merged from de novo assembly and IsoSeq sequence data.
Creator: Mojca Juteršek
Submitter: Mojca Juteršek
Arginine kinase has been thought of as a potential stress marker (see 'Metabolic changes by oxidative stress in T. b. brucei 427'), the gene knockout cells have been constructed.
Creators: Dong-Hyun Kim, Eduard Kerkhoven
Submitter: Dong-Hyun Kim
In order to construct an in vivo-like buffer for S. pyogenes, the intracellular concentrations of Fe, K, Mg, Mn Na, P and S elements were determined via ICP-AES (inductively coupled plasma atomic emissionspectroscopy) method at the Institute of Land Use, University of Rostock. The samples for the analysis were obtained from a steady state culture grown on CDM-LAB with glucose.
Creator: Araz Zeyniyev
Submitter: Araz Zeyniyev
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Data for three biological replicates of control culture and 37°C and 57°C in the file.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
B. subtilis was grown in M9 media with glucose as carbon source and the samples for RNA were harvested at OD600nm- 0.4 , 1.3 and 1.0 ). Culture was done at 37°C and samples at OD600nm- 0.4(Exponential), OD600nm- 1.3 (Early stationary), OD600nm-1.0(Late Stationary). All the samples were analysed for transcriptome as biological triplicates.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
- automated integration of transcriptomic and reactome data to differential equations
- structure of the paths is maintained
- continuous fermentation model in standard format for data integration, two component model (cell and fermenter)
call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example
where model_map is the desired mapping of species, reaction_compounds_final.csv is the entire network, extracellular.txt is a manual ...
Creator: Sebastian Curth
Submitter: Sebastian Curth
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_7, version 2
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_83, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_84, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_85, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_86, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_87, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_88, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_89, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_89, version 2
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_90, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_91, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_92, version 1
Creators: BioData SynthSys, Carl Troein, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_77, version 1
Creators: BioData SynthSys, Daniel Seaton
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_78, version 1
Creators: BioData SynthSys, Daniel Seaton
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_79, version 1
Creators: BioData SynthSys, Daniel Seaton
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Creator: Fatemeh Zamanzad Ghavidel
Submitter: Fatemeh Zamanzad Ghavidel
In response to the COVID-19 pandemic, the Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 45,000 scholarly articles, including over 33,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.
This dataset is intended to mobilize researchers to apply recent advances in natural language processing to generate new insights in ...
Creator: Allen Institute For AI, Anthony Goldbloom, Peijen Lin, Paul Mooney, Carissa Schoenick, Sebastian Kohlmeier, devrishi, Timo Bozsolik, Ben Hamner
Submitter: Martin Golebiewski
Quantification of CPM and TCP concentrations in cod liver and bile using gas chromatography
Creator: Karina Dale
Submitter: Karina Dale
Meta data file, Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/meta/crispr_metadata.txt
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
The structure of was Transaminase of gamma-proteobacterium deposited in PDB under the code: 7p3t
Creator: Eleni Konia
Submitter: Ioannis Metaxas
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Digitized pharmacokinetics data.
Creator: Matthias König
Submitter: Matthias König
Contains exp.csv, a collection of experimental data of CholineChloride:Glycerol:Water mixtures. Contains sim.csv, a collection of molecular dynamics simulation data of CholineChloride:Glycerol:Water mixtures. Contains Modelling_exp_Figure3.csv, a collection of modelled Eeta (energy activation of viscous flow), lnEta0 (viscosity at infinite temperature) values of CholineChloride:Glycerol:Water mixtures, based on experimental data, see the associated publication for details. Contains ...
Creator: Xinmeng Xu
Submitters: Gudrun Gygli, Xinmeng Xu
The classification in reproducible and not reproducible models was made by Tiwari et al.
Citations were looked up in Scopus, Web of Science and Google Scholar.
The following journals had to be excluded, as Journal Impact Factors (JIF) were missing or papers were discontinued:
- Experientia was closed 1996 and continued as Cellular and Molecular Life Sciences 1997
- The American journal of physiology – split into fields 1977, further splits in 1980 and 1989
- IFAC Proceedings Volumes – last issue ...
Creator: Sebastian Höpfl
Submitter: Sebastian Höpfl
Kinetic entry 14792 SBML for query http://sabiork.h-its.org/sabioRestWebServices/kineticLaws/14792
Creator: Matthias König
Submitter: Matthias König
Supplementary File S2: Kinetic entries for human galactose metabolism. SBML for query: http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/sbml?q=Pathway:%22galactose%20metabolism%22%20AND%20Organism:%22homo%20sapiens%22
Creator: Matthias König
Submitter: Matthias König
Measured in cod liver by the ELISA method, in Atlantic cod exposed to PAHs and PFASs
Creator: Karina Dale
Submitter: Karina Dale
CYP1A2: Generic Classification 128
Creators: Uta Dahmen, Mohamed Albadry
Submitter: Mohamed Albadry
CYP2E1: Generic Classification 128
Creators: Mohamed Albadry, Uta Dahmen
Submitter: Mohamed Albadry
CYP3A4: Generic Classification 128
Creators: Mohamed Albadry, Uta Dahmen
Submitter: Mohamed Albadry
TRK1, TRK2
Creator: Silvia Petrezselyova
Submitter: The JERM Harvester