cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100287
title: Supporting data for "ReGaTE, Registration of Galaxy Tools in Elixir"

description: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work, and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and work flow environments have accelerated, to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse.
We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend API to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry.
ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services, whilst enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github, at
https://github.com/C3BI-pasteur-fr/ReGaTE.
DOI: 10.5524/100293
title: Software for "MetaLIMS, A Simple Open-Source Laboratory Information Management System for Small Metagenomic Labs"

description: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated IT position, so LIMS must also be easy to setup and maintain with minimal technical proficiency.<br>
MetaLIMS is a free and open source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information the user can also add fields specific to the users lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web-deployment, MetaLIMS options the use of commercial web-hosting combined with MetaLIMS bash scripts for ease of set-up. <br>
MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.
DOI: 10.5524/100294
title: Supporting data for "Laboratory X-ray micro-computed tomography: a user guideline for biological samples"

description: Laboratory X-ray micro-computed tomography (micro-CT) is a fast growing method in scientific research applications that allows for non-destructive imaging of morphological structures. This paper provides an easily operated "how-to" guide for new potential users and describes the various steps required for successful planning of research projects that involve micro-CT. Background information on micro-CT is provided, followed by relevant set-up, scanning, reconstructing and visualization methods and considerations. Throughout the guide, a Jackson's chameleon specimen which was scanned at different settings is used as an example. The ultimate aim of the paper is make new users familiar with the concepts and applications of micro-CT in an attempt to promote its use in future scientific studies.
DOI: 10.5524/100295
title: Supporting data for "EEG datasets for motor imagery brain computer interface"

description: Most investigators of brain computer interface (BCI) believe that BCI can be achieved through induced neuronal activity from the cortex, but not by evoked neuronal activity. Motor imagery (MI) based BCI is one of the standard concepts of BCI, in that the user can generate induced activity by imagining motor movements. However, variations in performance over sessions and subjects are too severe to overcome easily; therefore, a basic understanding and investigation of BCI performance variation is necessary to find critical evidence of performance variation.<br>Here we present not only EEG datasets for MI BCI from 52 subjects, but also the results of a psychological and physiological questionnaire, EMG datasets, the locations of 3D EEG electrodes, and EEGs for non-task related states. <br>We validated our EEG datasets by using the percentage of bad trials, event-related desynchronization/synchronization (ERD/ERS) analysis, and classification analysis. After conventional rejection of bad trials, we showed contralateral ERD and ipsilateral ERS in the somatosensory area, which are well-known patterns of MI. Finally, we showed that 73.08% of datasets (38 subjects) included reasonably discriminative information.<br>Our EEG datasets included information necessary to determine statistical significance; they consisted of well-discriminated datasets (38 subjects) and less-discriminative datasets. These may provide researchers with opportunities to investigate human factors related to MI BCI performance variation, and may also achieve subject-to-subject transfer by using metadata, including a questionnaire, EEG coordinates, and EEGs for non-task related states. <br>
DOI: 10.5524/100299
title: Data supporting analysis of evolution of SET genes in insects

description: The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain-containing genes (SET genes) in all of the 147 arthropod genomes sequenced so far to understand the evolutionary history by which SET domain have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, which is ancestral to arthropod animals and specifically diversified during insect evolution. Considering that pseudogenization is the most probable fate of the new emerging gene copies, we provided experimental and evolutionary evidence to demonstrate their essential functions. Fluorescence in situ hybridization analysis and in vitro methyltransferase activity assays showed that the SmydA-2 gene was transcriptionally active and retained the original histone methylation activity. Expression knockdown by RNA interference significantly increased mortality, implying that the SmydA genes may be essential for insect survival. We further showed predominantly strong purifying selection on the SmydA gene family and a potential association between the regulation of gene expression and insect phenotypic plasticity by transcriptome analysis. Overall, these data suggest that the SmydA gene family retains essential functions that may possibly define novel regulatory pathways in insects. This work provides insights into the roles of lineage-specific domain duplication in insect evolution.
DOI: 10.5524/100302
title: Supporting data for "Deep whole-genome sequencing of 90 Han Chinese genomes"

description: Next generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data, due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low frequency and novel variants. Although whole exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole genome sequencing data is limited for any population, and a large amount of low-frequency, population-specific variants remains uncharacterized.
We have performed whole genome sequencing at high depth (~80X) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genome Project samples, including 45 North Han Chinese and 45 South Han Chinese samples. 83 of these 90 have not been sequenced by the 1000 Genomes Project. We have identified 12,568,804 single nucleotide polymorphisms, 2,074,734 short InDels and 26,142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7,007,685 novel variants with low frequency (defined as minor allele frequency &lt; 5%), including 5,816,839 SNPs, 1,172,919 InDels, and 17,927 structural variants.
Using deep sequencing data, we have built a greatly expanded spectrum of genetic variation for the Han Chinese genome. Compared to the 1000 Genomes Project, this Han Chinese deep sequencing data enhances characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement for the 1000 Genomes Project, as well as for other human genome projects.
DOI: 10.5524/100305
title: Supporting data for "The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet"

description: The blunt snout bream, Megalobrama amblycephala, is an economically important cyprinid fish species. As a herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is a less desirable feature for fish meat processing and consumption. <br>
As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala, with 779.54 Mb anchored on 24 linkage groups. Integrating spatiotemporal transcriptome analyses we show that intermuscular bone is formed in the more basal teleosts by intramembranous ossification, and may be involved in muscle contractibility and coordinating cellular events. Comparative analysis revealed that olfactory receptor genes, especially of the beta type, underwent an extensive expansion in herbivorous cyprinids, whereas the gene for the umami receptor T1R1 was specifically lost in M. amblycephala. The composition of gut microflora, which contributes to the herbivorous adaptation of M. amblycephala, was found to be similar to that of other herbivores.<br>
As a valuable resource for improvement of M. amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation.
DOI: 10.5524/100306
title: Supporting data for "Lipidomic profiling reveals distinct differences in plasma lipid composition in healthy, prediabetic and type 2 diabetic individuals"

description: The relationship between dyslipidemia and type 2 diabetes (T2D) has been extensively reported, but the global lipid profiles, especially in the East Asia population, associated with the development of T2D remain to be characterized. <br>Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was applied to detect the global lipidome in fasting plasma of 293 Chinese individuals, including 114 T2D patients, 81 prediabetic subjects and 98 individuals with normal glucose tolerance (NGT). Both qualitative and quantitative analyses revealed a gradual change in plasma lipid features going from NGT individuals over prediabetic to T2D individuals with T2D patients exhibiting characteristics close to those in prediabetic individuals, whereas they differed significantly from individuals with NGT. We constructed and validated a random forest (RF) classifier with 28 lipidomic features that effectively discriminated T2D from NGT or prediabetes. The majority of the selected features showed significant correlations with diabetic clinical indices.<br>Hydroxybutyrylcarnitine was positively correlated with fasting plasma glucose (FPG), 2-hour postprandial glucose (2h-PG), glycated hemoglobin (HbA1c) and insulin resistance index (HOMA-IR), and lysophosphatidylcholines such as LysoPC (18:0), LysoPC (18:1) and LysoPC (18:2) were all negatively correlated with HOMA-IR.
DOI: 10.5524/100308
title: Supporting data for "Genome Annotation Generator: A simple tool for generating and correcting WGS annotation tables for NCBI submission"

description: One of the most overlooked, yet critical components of a whole genome sequencing project is the submission and curation of the data to a genomic repository, most commonly NCBI. While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into NCBIs annotation table format, these tools typically require back-end setup and connection to an SQL database and/or some knowledge of programming (Perl, Python) to implement. With whole genome sequencing becoming commonplace, genome sequencing projects are moving away from the genome centers, and into the ecology or biology lab, where much less resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, transfer annotations, and convert a draft genome assembly and annotation set into NCBI annotation table (.tbl) format, facilitating submission to NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms,
and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks.
<br>
The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline.
DOI: 10.5524/100261
title: Supporting data for "GUIdock-VNC: Using a graphical desktop sharing system to provide a browser-based interface for containerized software"

description: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line based tool and many bioinformatics pipelines consist of components that require a graphical user interface.
We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud.
As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead.
DOI: 10.5524/100264
title: Supporting data for "Stepwise Distributed Open Innovation Contests for Software Development - Acceleration of Genome-Wide Association Analysis"

description: The association of differing genotypes with disease related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low cost genotyping and sequencing has made collecting large scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies are being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies (GWAS) associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets. 
<br>
Using open innovation (OI) and contest based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in less than 6 months by providing rapid access to highly skilled programmers with specialized, difficult-to-find skill sets. Through a crowd based contest a combination of computational, numeric and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645863 variants, compared to PLINK 1.07s logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project.
DOI: 10.5524/100266
title: Supporting data for "Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history"

description: The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. 
We sequenced the genome of Tropilaelaps mercedesae, the prevalent ectoparasitic mite infesting honey bees in Asia and predicted 15,190 protein-coding genes which were well supported by the mite transcriptomes and proteomic data. Although amino acid substitutions have been accelerated within the conserved core genes of two mites, T. mercedesae and Metaseiulus occidentalis, T. mercedesae has undergone the least gene family expansion and contraction between the seven arthropods we tested. The number of sensory system genes has been dramatically reduced but T. mercedesae contains all gene sets required to detoxify xenobiotics. T. mercedesae is closely associated with a symbiotic bacterium (Rickettsiella grylli-like) and DWV, the most prevalent honey bee virus. 
T. mercedesae has a very specialized life history and habitat as the ectoparasitic mite strictly depends on the honey bee inside a stable colony. Thus, comparison of the genome and transcriptome sequences with those of a tick and free-living mites has revealed the specific features of the genome shaped by interaction with the honey bee and colony environment. Genome and transcriptome sequences of T. mercedesae, as well as Varroa destructor (another globally prevalent ectoparasitic mite of honey bee), not only provide insights into the mite biology, but may also help to develop measures to control the most serious pests of the honey bee.
DOI: 10.5524/100270
title: Supporting data for "Phenobook: An open source software for phenotypic data collection"

description: We have developed a novel, open source software called Phenobook, an easy, flexible and intuitive tool to organize, collect and save experimental data for further analyses. Phenobook was conceived to collect phenotypic observations in a user-friendly, cost-effective way. It consists of a web-based software for experiment design, data input and visualization, and exportation, combined with a mobile application for remote data collecting. We provide in this article a detailed description of the developed tool.<br>
Phenobook is a software tool that can be easily implemented in collaborative research and development projects involving data collecting and forward analyses. Adopting Phenobook is expected to improve the involved processes by minimizing input errors, resulting in higher quality and reliability of the research outcomes.
DOI: 10.5524/100271
title: Data and analysis of diet-induced and obesity-associated alterations of gut microbiota of 129S6/Sv and C57BL/6J mice

description: It is well known that the microbiota of high fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity. <br>Using HiSeq-based whole genome sequencing we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low fat or HF diets with or without supplementation with the COX-inhibitor, indomethacin. <br> Here we present the sequence assemblies and annotations for those 54 samples, together with the gene catalogue and relevative abundance levels of both genes and OTUs. It is hoped these data can be used for comparison in future studies of a similar design.
DOI: 10.5524/100273
title: Supporting data for "Orthogonal Decomposition of Left Ventricular Remodelling in Myocardial Infarction"

description: Left ventricular size and shape is important for quantifying cardiac remodelling in response to cardiovascular disease. Geometric remodelling indices have been shown to have prognostic value in predicting adverse events in the clinical literature, but these often describe interrelated shape changes. We developed a novel method for deriving orthogonal remodelling components directly from any (moderately independent) set of clinical remodelling indices. 
Six clinical remodelling indices (end-diastolic volume index, sphericity, relative wall thickness, ejection fraction, apical conicity and longitudinal shortening) were evaluated using cardiac magnetic resonance images of 300 patients with myocardial infarction, and 1,991 asymptomatic subjects, obtained from the Cardiac Atlas Project. Using these Remodelling scores were calculated quantify the amount of each remodelling component in each case. The data and analyses are available from www.cardiacatlas.org.