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  • Data include: Sequences from parasites belong to two genera of Haemosporidia. Hematocrit and white blood cell counts from the host during the experiment. Band count and PCR score from the triplicate molecular diagnosis (before and after the MG infection)
    Data Types:
    • Sequencing Data
    • Tabular Data
    • Dataset
  • Dataset used to reconstruct the phylogenetic relationships among spaghetti worms and their allies (Terebelliformia, Annelida). The datasets comprise transcriptomic matrices, a matrix of Sanger sequenced genes and a matrix of morphological characters.
    Data Types:
    • Other
    • Software/Code
    • Sequencing Data
    • Tabular Data
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    • Document
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    • File Set
  • This dataset consists of 348 non-zero onset Vietnamese speeches (with their transcripts and the labelled start and end times of each speech) extracted from approximately 30-hour of FPT Open Speech Data (released publicly in 2018 by FPT Corporation). The extraction process was done automatically by a Python program written by the contributor. The speeches are in *.mp3 format and *.wav format (Mono, 48 kHz, 32-bit float) while the transcript file is in *.txt format with utf-8 encoding scheme. The dataset is useful for any onset detection research and development since the start and end times of each speech are already labelled. Copyright 2018 FPT Corporation Permission is hereby granted, free of charge, non-exclusive, worldwide, irrevocable, to any person obtaining a copy of this data or software and associated documentation files (the “Data or Software”), to deal in the Data or Software without restriction, including without limitation the rights to use, copy, modify, remix, transform, merge, build upon, publish, distribute and redistribute, sublicense, and/or sell copies of the Data or Software, for any purpose, even commercially, and to permit persons to whom the Data or Software is furnished to do so, subject to the following conditions: The above copyright notice, and this permission notice, and indication of any modification to the Data or Software, shall be included in all copies or substantial portions of the Data or Software. THE DATA OR SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE DATA OR SOFTWARE OR THE USE OR OTHER DEALINGS IN THE DATA OR SOFTWARE. Patent and trademark rights are not licensed under this FPT Public License.
    Data Types:
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  • Hardware design for build a Step Width System Capture
    Data Types:
    • Other
    • Software/Code
    • Geospatial Data
    • Image
    • Sequencing Data
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    • Dataset
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    • Audio
  • Different human linker histone (H1) variants are expected to have distinct binding modes to the nucleosome. The position and orientation of a number of different H1 globular domains on the nucleosome were investigated through molecular docking using MGLTools and HADDOCK. The nucleosome core and linker DNA in the GH5-chromatosome structure (PDB: 4QLC) were used as a docking template. GH5 (in PDB: 4QLC) was re-docked to this template to test the docking algorithm. Docked and re-docked GH5 compared well. The docking algorithm was further tested by docking the NMR solution structure of the globular domain of chicken H1 (GH1, PDB: 1GHC) to the nucleosome template. The position of docked GH1 on the nucleosome agreed with literature. 
The N-terminal - and globular domain H1x hybrid (NGH1x) was studied using solution NMR in both low (20 mM sodium phosphate, pH 7.0) and high (20 mM sodium phosphate, 1 M sodium perchlorate, pH 7.0) ionic strength conditions (de Wit, H., Vallet, A., Brutscher, B. et al. Biomol NMR Assign (2019) 13: 249. https://doi.org/10.1007/s12104-019-09886-x). These low and high ionic strength structures were docked to the nucleosome template. 
Homology (MODELLER) and ab initio modeling (CS-ROSETTA) were employed to model structures for other human H1 globular domains: GH1.0, GH1.4, GH1oo, and GH1t. The modeled structures were also docked to the nucleosome template.
 All the docking procedures listed above produced 100 models of different energies. In each case, the lowest energy docked model was chosen. The structures of all the H1 globular domains that were docked to the template are given as PDB files (1GHC_lowest_energy.pdb; 2LSO_lowest_energy.pdb; GH5_re-docked_position.pdb; NGH1x_high_salt_NTD.pdb; NGH1x_low_salt_NTD.pdb; modeled_GH1_0_lowest_energy.pdb; modeled_GH1_4_lowest_energy.pdb; modeled_GH1oo_lowest_energy.pdb; modelled_GH1t_lowest_energy.pdb) in the data file. The nucleosome template structure is also given in PDB file format (4QLC_nucleosome_without_GH5.pdb). Finally, the docked models are also given (GH5-chromatosome.pdb; 1GHC-chromatosome.pdb; 2LSO-chromatosome.pdb; GH1_0-chromatosome.pdb; GH1_4-chromatosome.pdb; GH1oo-chromatosome.pdb; GH1t-chromatosome.pdb; NGH1x_no_salt-chromatosome.pdb; NGH1x_salt-chromatosome.pdb). The files are compatible with most molecular graphics software. The file Dockings_modelling_test_and_results.pdf provides the modeling and docking results in figures and tables. A short description of each figure and table is given within the PDF file.
    Data Types:
    • Sequencing Data
    • Dataset
    • Document
  • The procreative statistical framework of musical note structures produces a crucial role in multimedia music classification and reconstruction strategies. Another most significant thing for harmonious music composition is the rhythmic structures that provide musical performance in a harmonic form. This paper has illustrated computational music theory and allied factors to regulate what human beings can acquire, remember, and reconstruct music for sustaining intangible cultural heritage. The music strings or symbols are also imperative factors that assist the musicians as performance guidelines. To afford a syntactic outline of musical note arrangements, a stochastic model along with probabilistic context-free music grammar has been illustrated in this paper. The state transition analysis has also been incorporated in terms of transition table and diagram to demonstrate which state can move to the other one within a finite automaton depending on the behaviors of the current state and associated transition rule. Petri net has been used for modeling and simulating the projected complex music composition framework to analyze system performances. The Petri net simulation-based reachability and system efficiency have been evaluated for analyzing the effectiveness of the proposed event-driven architecture. For incorporating real data into the projected framework, the music composition and reconstruction tool has also been demonstrated. The system performance evaluation metric has shown that around 92% efficiency level has been achieved by analyzing the projected music composition model.
    Data Types:
    • Tabular Data
    • Dataset
    • Document
    • Audio
  • Variant call file of DENV2 16681 passage 1 in M3 iPSC cells (open with Microsoft Excel)
    Data Types:
    • Sequencing Data
    • Dataset
  • This data includes all the input data for the test instances used in the experiments. The input data consists of three sets of benchmarks including OR-Lib set (40 graphs), TSP-Lib set (20 graphs) and University of Florida Sparse Matrix Collection (3 graphs) .
    Data Types:
    • Dataset
    • Text
    • Audio
  • The Indeterminate Domain (IDD) proteins are a plant specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development; however the function of most of IDDs is unknown and its molecular evolution has not been explored. Here, Prochetto and Reinheimer reconstructed the evolution of IDDs during plant land conquest. They found that IDDs arose from the common ancestor of Streptophyta. Once in land, IDDs experienced a rapid radiation that accompanied key morphological, physiological and biochemical transitions required in plant terrestrialization. The authors present a solid phylogenetic framework of annotated IDD genes which links genetic and functional knowledge from model to non-model species.
    Data Types:
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    • Sequencing Data
    • Tabular Data
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    • Text
  • Data from: Bitomský M., Mládková P., Pakeman RJ, & Duchoslav M. (2020). Clade composition of a plant community indicates its phylogenetic diversity. Ecology and Evolution. doi: 10.1002/ece3.6170 Data summarises results from the case studies and simulations presented in our paper. In addition, we provide an R script for calculation of proposed phylogenetic diversity metrics (the clade indices). Brief description of each file: 1. Grasslands_DNA_markers_info.xls - Accession numbers of all DNA markers used for phylogeny inference in grasslands 2. Grasslands_DNA_alignment_BEFORE_GBlocks.fasta - DNA alignment matrix before utilisation of the GBlocks tool 3. Grasslands_DNA_alignment_AFTER_GBlocks.fasta - DNA alignment matrix after utilisation of the GBlocks tool 4. Grasslands_BEAST_file.xml - BEAST .xml file submitted to the CIPRES portal (www.phylo.org) 5. Grasslands_tree.txt - Dated MCC tree, grasslands (newick format) 6. Grasslands_tree.nex - Dated MCC tree, grasslands (nexus format) 7. Phyto-database_pruned_tree.txt - Pruned dated tree from the super tree of European flora (Durka & Michalski 2012, Ecology), phytosociological database (newick format) 8. Plot_data.slx - plot data of all case studies + species lists 9. Simulation_results.txt - Summary of R2 values (phylogeny-based metric ~ the clade index) for simulated phylogenies and community matrices (manipulated: phylogenetic scale, species pool size and species richness range) 10. Bitomsky2020EE_R_script_indices.R - An R script for computation of the clade indices (with notes and examples)
    Data Types:
    • Software/Code
    • Sequencing Data
    • Tabular Data
    • Dataset
    • Document
    • Text