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Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the the M-loop region of a Leishmania donovani alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering). No result was obtained for compound 6.
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the interface region between two neighboring alpha-tubulin monomers of Leishmania donovani; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilaments of the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region residue ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the N-loop region of a Leishmania donovani alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Leishmania donovani multimeric alpha-tubulin protein receptor for docking studies, generated by alignment of two identical models of L. donovani alpha-tubulin on template 5ubq alpha-tubulin chains of two neighboring protofilaments (A, C).
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the M-loop region of a Leishmania infantum alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the interface region between two neighboring alpha-tubulin monomers of Leishmania infantum; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilaments of the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the N-loop region of a Leishmania infantum alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Leishmania infantum multimeric alpha-tubulin protein receptor for docking studies, generated by alignment of two identical models of L. infantum alpha-tubulin on template 5ubq alpha-tubulin chains of two neighboring protofilaments (A, C).
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Creators: None
Submitter: Lorenzo Tagliazucchi
Creators: None
Submitter: Lorenzo Tagliazucchi
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Lactobacillus plantarum strains WCFS1, NC8, JDM1 and ATCC 14917 amino acid concentrations mM supernatant, high (D=0.4) and low (D=0.05) growth rates
Creator: Anette McLeod
Submitter: Anette McLeod
Lactobacillus plantarum ATCC 14917 differentially expressed proteins, comparison between low and high growth rates
Creator: Anette McLeod
Submitter: Anette McLeod
Lactobacillus plantarum, 4 strains (WCFS1, NC8, ATCC 14917, JDM1) chemostat experiments low and high growth rates, OD and DW measurements
Creator: Anette McLeod
Submitter: Anette McLeod
Lactobacillus plantarum strains WCFS1, NC8, ATCC14917, JDM1. HPLC end products mM measurements (CDM subtracted) and flux calculations, high and low growth rates.
Creator: Anette McLeod
Submitter: Anette McLeod
Lactobacillus plantarum JDM1 differentially expressed proteins, comparison between low and high growth rates
Creator: Anette McLeod
Submitter: Anette McLeod
Lactobacillus plantarum NC8 differentially expressed proteins, comparison between low and high growth rates
Creator: Anette McLeod
Submitter: Anette McLeod
Lactobacillus plantarum WCFS1 differentially expressed proteins, comparison between low and high growth rates
Creator: Anette McLeod
Submitter: Anette McLeod
Experimental data, in MATLAB binary file format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Biomass and metabolite data for Laurel and Hardy 1.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Model simulation data for Laurel and Hardy 1, in MATLAB binary format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.
Starch levels in carbon units (not C6) measured on on ...
Creators: Daniel Seaton, Yin Hoon Chew, Virginie Mengin
Submitter: Andrew Millar
Complete excel spradsheets for Laurel and Hardy 2, including data for the pgm mutant that were not analysed in the Chew et al. 2017 preprint/publication. Data include fresh and dry biomass, gas exchange, leaf numbers and metabolites in Col0 (WT), prr7prr9, pgm and lsf1 plants. Metabolite data are from plants after 27 days of growth (end of night) and 28 days (end of day and end of night).
Creators: Yin Hoon Chew, Virginie Mengin, Daniel Seaton
Submitter: Daniel Seaton
Experimental data for Laurel and Hardy 2, in MATLAB binary format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Mean and SD data for metabolites and biomass, along with metadata used to simulate this experiment.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Simulation data for Laurel and Hardy 2, in MATLAB binary format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.
Starch levels in carbon units (not C6) measured on on ...
Creators: Yin Hoon Chew, Daniel Seaton, Virginie Mengin
Submitter: Andrew Millar
Excel spreadsheets for biomass, leaf number, gas exchange and metabolites, including pgm and lhycca1. Key data are for 27-28 day old plants for Col and prr7prr9, analysed for the preprint/publication. Gas exchange data for lhycca1 showed lower Assimilation per unit area than Col, prr7prr9; A in pgm was higher than Col. Metabolite data were also collected for Col and lhycca1 at 18 days, before the lhycca1 flowered, but these are marked as unreliable.
Creators: Yin Hoon Chew, Virginie Mengin, Daniel Seaton
Submitter: Daniel Seaton
Experimental data for Laurel and Hardy 3, in MATLAB binary format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Creator: Daniel Seaton
Submitter: Daniel Seaton
Simulation data for Laurel and Hardy 3, in MATLAB binary format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.
Starch levels in carbon units (not C6) measured on on days ...
Creators: Daniel Seaton, Yin Hoon Chew, Virginie Mengin
Submitter: Andrew Millar
Experimental data set for the kinetic characterisation of LDH
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Data for Fig. Supp 7B in Chew et al. PNAS 2014 Leaf number of the growing rosettes, from 5 to 37 days after sowing. Data and also results of three FMv1 model simulations, with default, fitted and linear (i.e. no juvenile-adult transition in phyllochron)
Creator: Yin Hoon Chew
Submitter: Andrew Millar
Data for Figs 3C, 3F and Supp 2 in Chew et al. PNAS 2014 Leaf number of the growing rosettes, from 4 to 37 days after sowing (DAS). Data and also results of FMv1 model simulations. Note that Fei-0 was previously tested by Mendez-Vigo et al, suggesting this line had a higher leaf appearance rate. We suggested that its larger final leaf number was more likely due to faster germination.
Creator: Yin Hoon Chew
Submitter: Andrew Millar
This excel template is for use of describing HCS microscopy data. It was created based on ISA methodology and modified to conform REMBI recomandations.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Comparison between axenic and planktonic readcounts with deseq2
Creator: Malte Herold
Submitter: Malte Herold
Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta
Creator: Malte Herold
Submitter: Malte Herold
Comparison for LFQs with t-test in Perseus
Creator: Malte Herold
Submitter: Malte Herold
Repository for omics data analysis
Creator: Malte Herold
Submitter: Malte Herold
Table combining data for L.ferriphilum. RNAseq data, Proteomics LFQs, Functional annotation
Creator: Malte Herold
Submitter: Malte Herold
Creator: Malte Herold
Submitter: Malte Herold
Creator: Malte Herold
Submitter: Malte Herold
Creator: Malte Herold
Submitter: Malte Herold
LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed
Creators: Malte Herold, Ansgar Poetsch, Mohamed El Hajjami, Ansgar
Submitter: Malte Herold
LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed
Creators: Malte Herold, Ansgar Poetsch, Mohamed El Hajjami
Submitter: Malte Herold
Raw read files for samples
Creator: Malte Herold
Submitter: Malte Herold
Normalized counts (tpm) for L.ferriphilum samples from continuous culture.
Creator: Malte Herold
Submitter: Malte Herold
Normalized counts (tpm) for LF samples with mineral
Creator: Malte Herold
Submitter: Malte Herold
Raw data and assembly for pacbio sequencing of L.ferriphilum.
Creator: Malte Herold
Submitter: Malte Herold
Creator: Lorenzo Tagliazucchi
Submitter: Lorenzo Tagliazucchi
Creator: Lorenzo Tagliazucchi
Submitter: Lorenzo Tagliazucchi
LFQ intensities derived from proteomics measurements
Creator: Malte Herold
Submitter: Malte Herold
Creator: Fatemeh Zamanzad Ghavidel
Submitter: Fatemeh Zamanzad Ghavidel
Linked with model: 10.15490/fairdomhub.1.model.802.1
Creators: None
Submitter: James Wordsworth
Linked with model: 10.15490/fairdomhub.1.model.802.1
Creators: None
Submitter: James Wordsworth
Linked with Model: 10.15490/fairdomhub.1.model.802.1
Creators: None
Submitter: James Wordsworth
Data file for PLaSMo accesssion ID PLM_4, version 1
Creators: BioData SynthSys, Robert Muetzelfeldt
Submitter: BioData SynthSys
Salmon feed switch experiment: Lipid class quantitation for gut tissue samples (POS mode).
Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Salmon feed switch experiment: Lipid class quantitation for liver tissue samples (POS mode).
Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Salmon feed switch experiment: Lipid class quantitation for muscle tissue samples (POS mode).
Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Salmon feed switch experiment: Lipid identification for gut tissue samples (POS mode).
Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.
The 'O-' prefix ...
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Salmon feed switch experiment: Lipid identification for liver tissue samples (POS mode).
Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.
The 'O-' ...
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Salmon feed switch experiment: Lipid identification for muscle tissue samples (POS mode).
Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.
The 'O-' ...
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Results of lipid species (expressed in pmol) determined in cod liver microsomes exposed to PAH and PFAS
Creators: Karina Dale, Alejandra Gilabert
Submitter: Karina Dale
Full list of detected miRNA which were found to be deregulated in PE-EVs.
Creator: Natalia Gebara
Submitter: Natalia Gebara
Participants of 2nd FAIRDOM PALs meeting in Munich
Creators: Olga Krebs, Wolfgang Müller, Rostyslav Kuzyakiv
Submitter: Olga Krebs
List of participants/1st EraSysApp PALs meeting
Creator: Olga Krebs
Submitter: Olga Krebs
List of publications from 2006 till 2016. Note: I retired from the University of Amsterdam in 2010
Creator: Roel Van Driel
Submitter: Roel Van Driel
This Excel file contains lists of model (Comprehensive model for COVID-19) reactions and species in table format Comprehensive model for COVID-19 coused by SARS-CoV-2
Creators: Alexey Kolodkin, Hans V. Westerhoff
Submitter: Alexey Kolodkin
Publications and patents from the last 6 years
Creator: Vitor Martins dos Santos
Submitter: Vitor Martins dos Santos
Creator: Stefan Henrich
Submitter: Stefan Henrich
Concentrations of various contaminants in liver from cod caged in Kollevåg and at reference location.
Creators: None
Submitter: Karina Dale
EROD activity in liver of cod exposed to chlorpyrifos-methyl
Creator: Karina Dale
Submitter: Karina Dale
Mean normalized expression (MNE) levels of cyp1a and acox1 measured in liver of Atlantic Cod exposed to PAH and PFAS mixtures
Creator: Karina Dale
Submitter: Karina Dale
Read counts for each sample
Creators: Graceline Tina Kirubakaran, Fabian Grammes, Gareth Gillard
Submitter: Graceline Tina Kirubakaran
Creators: Graceline Tina Kirubakaran, Gareth Gillard, Fabian Grammes, Jon Olav Vik
Submitter: Graceline Tina Kirubakaran
FPKMs or Fragments Per Kilobase of exon per Million reads . Fragment means fragment of DNA, so the two reads that comprise a paired-end read count as one. Per kilobase of exon means the counts of fragments are then normalized by dividing by the total length of all exons in the gene (or transcript). This bit of magic makes it possible to compare Gene A to Gene B even if they are of different lengths. Per million reads means this value is then normalized against the library size. This bit of magic ...
Creators: Graceline Tina Kirubakaran, Fabian Grammes, Gareth Gillard
Submitter: Graceline Tina Kirubakaran
PDB file of the prepared Leishmania major dihydrofolate reductase docking receptor based on a published homology model of LmDHFR (Panecka-Hofman et al. (2017) Biochim Biophys Acta Gen Subj. 1861(12), 3215-3230. DOI: 10.1016/j.bbagen.2017.09.012) without water molecules.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
PDB file of the prepared Leishmania major pteridine reductase 1 docking receptor based on chain A of PDB-ID 1e92 with a conserved set of structural waters.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
PDB file of the prepared Leishmania major pteridine reductase 1docking receptor based on chain A of PDB-ID 1e92 without additional water molecules.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Batch sample publishing
Creators: None
Submitter: Jake Schissel
Data for local pH monitoring experiments for dissolution in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution
Creator: Jennifer Zehner
Submitter: Jennifer Zehner
Data for local pH monitoring precipitation experiments in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution
Creator: Jennifer Zehner
Submitter: Jennifer Zehner
Local sensitivity analysis based on 40 samples using 1000x sampling from measurement distribution. The control shown is the control over flux through glycolysis represented by flux through PRK. Th plot summarized the control for each parameter over all observed metabolite concentrations encountered for the 40 samples. As such the metabolic control analysis is local but shows the distribution taking into account measurement error as well as biological variation over the 40 samples.
Creators: None
Submitter: Niels Zondervan
Tab seperated file containing the raw output of the local sensitivity analysis based on 40 samples (based on 1000x sampled metabolite values) from the MEAN and SD of the metabolite measurements. Sensitivity analysis is based on the flux through PFK as objective and as proxy for flux through glycolysis. Data can be plotted using the R script "plotLocalGlobalSensitivity1.5.R" associated to the same assay.
Creators: None
Submitter: Niels Zondervan
Confocal microscopy of Arl1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.
Creator: Paul Heusden
Submitter: Paul Heusden
Confocal microscopy of CIN5-GFP from the collection of GFP strains at standard growth conditions (50 mM KCl)
Creator: Paul Heusden
Submitter: Paul Heusden
Confocal microscopy of Ena1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.
Creator: Paul Heusden
Submitter: Paul Heusden
Confocal microscopy of HOG1-GFP from GFP-strain collection under standard growth cionditions (50 mM KCl).
Creator: Paul Heusden
Submitter: Paul Heusden
Confocal microscopy of Nha1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.
Creator: Paul Heusden
Submitter: Paul Heusden
Confocal microscopy of Pma1-GFP cells after 60 min at 0 or 50 mM KCl .
Creator: Paul Heusden
Submitter: Paul Heusden
First selection of LOINC Codes for data extraction
Creators: Theresa Bender, Christian Bauer
Submitter: Theresa Bender
Raw data for L.ferriphilum biofilm proteomics data
Creator: Malte Herold
Submitter: Malte Herold
Raw proteomics data for L. ferriphilum planktonic samples
Creators: Malte Herold, Mohamed El Hajjami
Submitter: Malte Herold