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Data file for PLaSMo accesssion ID PLM_51, version 1
Creators: BioData SynthSys, Richard Adams
Submitter: BioData SynthSys
Creator: Tomas Fiedler
Submitter: The JERM Harvester
Data file for PLaSMo accesssion ID PLM_74, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Badly chosen substrate concentrations for an intital rate experiment give data that makes it difficult to fit with a kinetic model and judge the quality of the fit.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Very well chosen substrate concentrations for an intital rate experiment give data that makes it very easy to fit with a kinetic model and judge the quality of the fit.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Well chosen substrate concentrations for an intital rate experiment give data that makes it easy to fit with a kinetic model and judge the quality of the fit and use it as a basis for the final gold-round experiment.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
An initial choice of 5 widely spaced substrates enables a first, rough estimate of Km to inform the design of first-round experiments.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
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
Creators: None
Submitter: Jake Schissel
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
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
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Batch sample publishing
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
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
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Jake Schissel
Batch sample publishing
Creators: None
Submitter: Dikshant Pradhan
Batch sample publishing
Creators: None
Submitter: Dikshant Pradhan
Batch sample publishing
Creators: None
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Raw data for Ac + St leaching experiments proteomics data, with Ac 10x inoculum sizing
Creator: Malte Herold
Submitter: Malte Herold
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Jake Schissel
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
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Jake Schissel
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
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Contains the absolute copy number per locus tag during growth between 0.25 and 96hours of growth Growth in batch, cells attached to the bottom of the flask, non-aerated, non-stirred
Creators: Luis Serrano, Maria Lluch, Eva Yus
Submitter: Niels Zondervan
Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells exposed to methylene blue
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells under high pH stress (pH8.7)
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Intracellular concentrations of 50 metabolites measured by LC-MS using isotope ratio based mass spectrometry technique
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
This mini-symposium, colocated at the ECMTB in Gothenburg, presents the state-of-the-art in computational methods for multicellular systems biology. It brings together developers and users of this software to identify common approaches and future challenges concerning multiscale integration, model specification, model exchange, scalability, workflow management as well as compliance to standards and guidelines. The session thus aims to provide an overview of the available modeling and simulation ...
Creator: Walter de Back, TU Dresden
Submitter: Lutz Brusch
The Table represents the simulation results of how the presence of phosphate ions (Pi) in the solution might affect the activity of four LDH enzymes. This includes the algorithmic analysis of the binding energies values computed by the GRID program (see Part 4, model) for each enzyme in presence and absence of FBP molecule at pH 6 and 7. The analysis was performed by using the algorithm proposed in Part 5, model.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Activity assays in cell free extracts of S. solfataricus grown on either L-fucose or D-glucose and activity assays with recombinant proteins
Creators: Jacqueline Wolf, Katharina Kruse, Bettina Siebers, Theresa Kouril
Submitter: Jacqueline Wolf
The excel spreadsheet about the inherency of the size dependency of optical properties at the nanoscale
Creator: Ioannis Metaxas
Submitter: Ioannis Metaxas
The excel spreadsheet about the inherency of the size dependency of optical properties at the nanoscale
Creator: Ioannis Metaxas
Submitter: Ioannis Metaxas
TbTryS activity was measured at 37°C in the in vivo-like buffer. All substrate stock solutions were prepared in the in vivo-like buffer and the pH was adjusted to 7.0. The assays were performed in a final volume of 2 ml and contained 0.2 mM NADH, 1 mM phosphoenolpyruvate, 4 units pyruvate kinase, 4 units L-lactate dehydrogenase, 0.17 µM TbTryS, 2.1 mM ATP and varying amounts of GSH, and Spd.
Creator: Alejandro Leroux
Submitter: Alejandro Leroux
The file contains the initial rate measurements of TbTryS obtained under different substrate and product initial concentrations.
Creator: Alejandro Leroux
Submitter: Alejandro Leroux
Creators: None
Submitter: Flora D'Anna
Creators: None
Submitter: Flora D'Anna
Data file for PLaSMo accesssion ID PLM_51, version 1
Creators: BioData SynthSys, Richard Adams
Submitter: BioData SynthSys
Creator: Martin Golebiewski
Submitter: Martin Golebiewski
Agenda for the satellite data management tutorial of Synthetic Biology 2017.
Creator: Natalie Stanford
Submitter: Natalie Stanford
3rd ERASysAPP – EXCHANGE Day: Networking and Info Day for research projects of the first and second ERASysAPP calls
Creators: Olga Krebs, Katalin Zsuzsanna Nagy, Heide Marie Hess
Submitter: Olga Krebs
Final version of the Agenda: All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock.
Creators: None
Submitter: Olga Krebs
Experimental data set for the kinetic characterisation of ALD
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Biomass data for individual plants at day 35, fresh and dry weights, as well as mean and SD, from study Gibberellins 1
Creators: Yin Hoon Chew, Andrew Millar
Submitter: Andrew Millar
All of the above metadata in one file
Creator: Charles Demurjian
Submitter: Charles Demurjian
The purpose of this is using it in ModelXChange.
Creator: Wolfgang Müller
Submitter: Wolfgang Müller
Contains for all samples, mean metabolite concentration and shows enzyme concentration used in model fitting and simmulations. Only metabolite present in the model are shown.
Creator: Niels Zondervan
Submitter: Niels Zondervan
raw data OD600
Creator: Koen van Grinsven
Submitter: Koen van Grinsven
amino acid auxotrophies as determined for S. pyogenes, E. faecalis, L. lactis and L. plantarum (ATCC, NC8, JDM1 and WCFS1) subsequent inoculation (3x) in CDM
Creator: Koen van Grinsven
Submitter: Koen van Grinsven
raw data OD600 of amino acid auxotrophy exps S. pyogenes
Creator: Koen van Grinsven
Submitter: Koen van Grinsven
amino acid auxotrophy for streptococcus pyogenes in CDM-IMIKRO (not CDM-LAB) as function of final growth yield (OD600 at stationary phase) in 96well plates (200 ul culture)
Creator: Araz Zeyniyev
Submitter: Araz Zeyniyev
Sulfolobus solfataricus P2 was cultivated on 1 % Caseinhydrolysate. Samples of the culture supernatants were taken at regular intervalls and analyzed by GC-MS. To evaluate the stability of amino acids under cultivation conditions an additional non-inoculated control culture was also analyzed.
Creators: Jacqueline Wolf, Dietmar Schomburg, Meina Neumann-Schaal, Julia Hofmann
Submitter: Jacqueline Wolf
Creator: Margrete Solheim
Submitter: Margrete Solheim
Creators: John Raedts, Wouter Kuit
Submitter: John Raedts
_p_RNAinVAL/_I_01_LabTrials/_S_07_dec2016/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_04_Stages/_A_03_stages-RNAisol/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_02_jun2016-RNAisol/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_09_jun2017/_A_02_jun2017-RNAisol/
Creator: Marko Petek
Submitter: Marko Petek
Content:
- Compiled 15 columns annotation of P. cordatum (Dougan et al. 2022)
- Summary of predicted unknown proteins of P. cordatum
- Calculations of predicted unknown proteins of P. cordatum
Tab color: annotation, purple; unknowns, green
Creators: None
Submitter: Jana Kalvelage
S. pneumoniae Control1 DNA-Seq PE1
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae Control 1 DNA PE2
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae Control 2 DNA PE1
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae Control 2 DNA PE2
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae HPUra 1 DNA PE1
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae HPUra 1 DNA PE2
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae HPUra 2 DNA PE1
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae HPUra 2 DNA PE2
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae kanamycin DNA PE1
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae kanamycin DNA PE2
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
E. coli DNA-Seq Barcodes: control 1: GTGGCC control 2: GTTTCG Trimethoprim 1: CACTCA Trimethoprim 2: CAGGCG
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
E. coli RNA-Seq Barcodes: Control 1: AGTTCC Control 2: ATGTCA
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
E. coli RNA-Seq Barcodes: Trimethoprim 1: CCGTCC Trimethoprim 2: GTAGAG
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae RNA-Seq Barcodes: Control 1: CAGATC Control 2: ACTTGA
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
S. pneumoniae RNA-Seq Barcodes: HPUra 1: CAGATC HPUra 2: ACTTGA Kanamycin: AGTCAA
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
This document shows the ArcA phosphorylation levels at different aerobiosis units, measured using Phos-tag gels, western immunoblotting. Exposed films were quantitated using ImageJ and the results shown here.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
Collected PDB-files of homology models of alpha-tubulin, all based on T. thermophila tubulin PDB-ID 5ubq, chain A:
Includes models of the following dinitroaniline herbicide sensitive species (UniProt ID in brackets):
- C. reinhardtii (P09204)
- E. indica (O22347)
- L. donovani (I3W8N6)
- L. infantum (E9AGJ8)
- L. major (Q4QGC5)
- P. falciparum (P14642)
- S. viridis (Q65C79)
- T. brucei (Q4GYY5)
- T. cruzi (Q27352)
- T. gondii (P10873)
- Z. mays (P14640)
Includes models of the following dinitroaniline ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
This archive contains all results of the PIPSA analysis run in zipped form. It contains the following subfolders:
- apbs: Computed electrostatic potential grids, all log files and similarity matrices for the full protein and all sites.
- pdb2pqr: PQR files: conversion results after processing uploaded PDB files with pdb2pqr
- pdbs: Original uploaded PDB files
The following sites have been analyzed (provided are site center (based on T. cruzi model, Ca of the residue) and the sphere radius):
Blume ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Patrick Becker
Creators: None
Submitter: Patrick Becker
Creators: None
Submitter: Patrick Becker
Creator: Runyu Liang
Submitter: Runyu Liang
Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Raw data for Ac+St planktonic cells, leaching experiments with St 10x incoulum sizing
Creator: Malte Herold
Submitter: Malte Herold
Creator: Maike Bartholomae
Submitter: Maike Bartholomae
Raw data for , Ac + St or Lf + St planktonic cells from leaching experiments
Creator: Malte Herold
Submitter: Malte Herold
The parameters A and B were estimated for the function f(x)=x⋅e^(B-Ax) and the AUC was calculated for the decay phase only. For OH-Midazolam the fourth replicate in the 2 weeks condition has an outlier in the measurement after six hours (more than 2SD above the mean of this condition) and was omitted for the AUC calculation as this could not be fitted to an exponential decay.
Creators: None
Submitter: Sebastian Höpfl
Pride project for raw and search data for AXX-Cn samples: LNU-AXX-Si00-CnB-P-B6ST-Pr_180min LNU-AXX-Si00-CnB-P-B7ST-Pr_180min LNU-AXX-Si00-CnB-P-B8ST-Pr_180min
Creator: Malte Herold
Submitter: Malte Herold