cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100230
title: Wrapping FreeSurfer 6 for use in high-performance computing environments

description: The purpose of this project is to wrap the recon-all workflow from FreeSurfer 6.0 beta in a Python processing framework for neuroimaging data called Nipype. FreesSurfer, an image analysis suite, performs cortical reconstruction and volumetric segmentation. FreeSurfers recon-all workflow provides researchers a simple interface for automatically processing of MRI data. Currently recon-all makes command-line program calls to other FreeSurfer processes from a tcsh script. Nipype offers a framework in python for making command-line program calls that will allow for faster processing in a high-performance computing environment. This will allow high-performance computing environments to execute steps of the workflow that are independent of each other to be run in parallel. The wrapping of the workflow in Nipype will also allow for easier manipulation of the individual steps in the workflow.<br>FreeSurfers recon-all tcsh workflow was used to process a set of MRI images. Recon-all then output a list of commands used to process the MRI data. The output commands were placed in a Nipype workflow. If a command did not have a pre-existing Nipype interface, then one was created. In order to ensure that the two workflows were analogous the Nipype and the tcsh workflow were run on the same set of MRI images and the outputs were compared. The comparisons were carried out with SimpleITK for image files and VTK for surface files.<br>All output images and surfaces from FreeSurfers recon-all were identical to those of the Nipype workflow. The stats files were also shown to be equivalent. Less significant files, such as log files, were either not thoroughly compared or were not output by the Nipype workflow.<br>The created Nipype workflow was shown to be analogous to pre-existing FreeSurfer tcsh workflow. With further development, Nipype could serve as a complete replacement to the tcsh workflow. This would allow for easier development of the workflow by researchers. Thorough testing on the processing times of the workflows in a high performance environment has not yet been evaluated, but it is hypothesized that the Nipype workflow will perform much faster. The collaborations at the 2015 OHBM BrainHack meeting were instrumental in accomplishing this task. Collaborations with the FreeSurfer, Nipype, and Human Connectome teams allowed members of this project to quickly identify problems and avoid unnecessary failures.
DOI: 10.5524/100241
title: Supporting data for "The preprocessed connectomes project repository of manually corrected skullstripped T1-weighted anatomical MRI data"

description: Skull-stripping is the procedure of removing non-brain tissue from anatomical MRI data. This procedure is necessary for calculating brain volume and for improving the quality of other image processing steps. Developing new skull-stripping algorithms and
evaluating their performance requires <em>gold standard</em> data from a variety of different scanners and acquisition methods. We complement existing repositories with manually-corrected brain masks for 125 T1-weighted anatomical scans from the Nathan Kline Institute Enhanced Rockland Sample Neurofeedback Study.<br>
Skull-stripped images were obtained using a semi-automated procedure that involved skull-stripping the data using the brain extraction based on non local segmentation technique (BEaST) software and manually correcting the worst results. Corrected brain masks were added into the BEaST library and the procedure was reiterated until acceptable brain masks were available for all images. In total, 85 of the skull-stripped
images were hand-edited and 40 were deemed to not need editing. The results are brain masks for the 125 images along with a BEaST library for automatically skullstripping other data.<br>
Skull-stripped anatomical images from the Neurofeedback sample are available for download from the Preprocessed Connectomes Project. The resulting brain masks can be used by researchers to improve their preprocessing of the Neurofeedback data, and as training and testing data for developing new skull-stripping algorithms and evaluating the impact on other aspects of MRI preprocessing. We have illustrated the
utility of these data as a reference for comparing various automatic methods and evaluated the performance of the newly created library on independent data.
DOI: 10.5524/100243
title: Supporting data for "Analyzing climate variations on multiple timescales can guide Zika virus response measures"

description: The emergence of Zika virus (ZIKV) as a public health emergency in Latin America and the Caribbean (LAC) occurred during a period of severe drought and unusually high temperatures. Speculation in the literature exists that these climate conditions were associated with the 2015/2016 El Niño event and/or climate change but to date no quantitative assessment has been made. Analysis of related flaviviruses -such as dengue and chikungunya, which are transmitted by the same vectors- suggests that ZIKV dynamics is sensitive to climate seasonality and longer-term variability and trends. A better understanding the climate conditions conducive to the 2014-2016 epidemic may permit the development of climate-informed short- and long-term strategies for ZIKV prevention and control.<br>Using a novel timescale-decomposition methodology, we demonstrate that extreme climate anomalies observed in most parts of South America during the current epidemic are not caused exclusively by El Niño or climate change -as speculated-, but are the result of a particular combination of climate signals acting at multiple timescales. In Brazil, the heart of the epidemic, we find that dry conditions present during 2013-2015 are explained primarily by year-to-year variability superimposed on decadal variability, but with little contribution of long-term trends. In contrast, the extreme warm temperatures of 2014-2015 resulted from the compound effect of climate change, decadal and year-to-year climate variability.<br>Here we provide the data upon which we based our interpretations. As described in the manuscript these have been aquired from the full data, which are available at http://iridl.ldeo.columbia.edu/maproom/Health/index.html and http://datoteca.ole2.org/maproom/Sala_de_Salud-Clima/index.html.es <br>
DOI: 10.5524/100245
title: Three Bauhinia species transcriptome sequence data

description: Hong Kongs emblem is the beautiful Bauhinia flower and appears on our flag. This is the flower of the orchid tree Bauhinia blakeana, which was first discovered in Hong Kong. What many people may not know is that it is a sterile hybrid, and how and why it ended up in Hong Kong is shrouded in mystery.
<br>
One of the best ways to help uncover the secrets of any organism is by understanding its genetic makeup. Genomics, sequencing of the genetic code of organisms, provides a complete look into the genetic complement of any species. It is also one of the key technologies that will define the 21st century. While Hong Kong has made major advances in this field, the general public has a very poor awareness and understanding of what this field even is.
<br>
By bringing together the emblematic and mysterious Bauhinia flower and the power and knowledge of genome technology, we can build a bridge between science and community enlightening our understanding of this plants interesting biology and informing and educating the public about this exciting and rapidly advancing field.
<br>
To build such a collaborative endeavor, we are launching the Hong Kong genome project through which we will sequence the genome of the Hong Kong emblem to better understand where it came from; train local students to assemble and analyse the data crucial skills needed for this field to advance; and engage the public through local pride.
<br>
This will be the first Hong Kong genome project: funded by the public; sequenced in Hong Kong; assembled and analysed by local students; and directly shared with the public. We also welcome contributions and interest from the rest of the world, hoping this serves as a model to inspire and inform other national genome projects, and aid the development of crucial genomic literacy and skills across the globe, inspiring and training a new generation of scientists to use these tools to tackle the biggest threats to mankind: climate change, disease, and food security.<br>The data presented here are four transcriptome datasets: leaf and flower data from Bauhinia blakeana as well as leaf transcriptomes from the most likely parent species Bauhinia purpurea and Bauhinia variegata. Specimens were collected in Hong Kong, and sequenced at the laboratories of BGI Hong Kong using the Illumina HiSeq 4000 platform. RNA was extracted using protocols available at protocols.io (see: dx.doi.org/10.17504/protocols.io.gsnbwde). These data are made available here for analysis and the open-source teaching of transcriptomics analysis. <br>For more on the project see: http://bauhiniagenome.hk/
DOI: 10.5524/100256
title: Supporting data for "Genome sequencing of the winged midge, Parochlus steinenii, from the Antarctic Peninsula"

description: In the Antarctic, only two species of Chironomidae occur naturallythe wingless midge, Belgica antarctica, and the winged midge, Parochlus steinenii. B. antarctica is an extremophile with unusual adaptations. The larvae of B. antarctica are desiccation- and freeze-tolerant and the adults are wingless. Recently, the compact genome of B. antarctica was reported and it is the first Antarctic eukaryote to be sequenced. Although they occur naturally in the Antarctic with B. antarctica, the larvae of P. steinenii are cold-tolerant but not freeze-tolerant and the adults are winged. Differences in adaptations in the Antarctic midges are interesting in terms of evolutionary processes under an extreme environment. Herein, we provide another genome of an Antarctic midge to elucidate the evolution of these species. 
The draft genome of P. steinenii had a total size of 138 Mbp, comprising 9,513 contigs with an N50 contig size of 34,110 bp, and a GC content of 32.2%. Overall, 13,468 genes were predicted using the MAKER annotation pipeline, and gene ontology classified 10,801 (80.2%) predicted genes to a function. Compared to the assembled genome architecture of B. antarctica, that of P. steinenii was approximately 50 Mbp longer with 6.2-fold more repeat sequences, whereas gene regions were similarly compact as B. antarctica.
DOI: 10.5524/100211
title: Software and supporting material for: "RES-Scanner: a software package for genome-wide identification of RNA-editing sites"

description: High-throughput sequencing (HTS) provides a powerful resolution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to discriminate RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors.<br>
Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-Seq and DNA-Seq data from the same individuals or samples. RES-Scanner allows using both raw HTS reads and pre-aligned reads in BAM format as inputs. While inputs are HTS reads, RES-Scanner can invoke BWA to align reads to the reference genome automatically. To rigorously discriminate potential false positives resulted from genetic variants, we equip RES-Scanner with sophisticated statistical models to infer the reliability of homozygous genotypes called from DNA-Seq data. These models are applicable to samples from both a single individual and a pool of multiple individuals given that the ploidy information is known. In addition, RES-Scanner implements statistical tests to discriminate genuine RNA-editing sites from sequencing error, and provides a series of sophisticated filtering options to remove false positives resulted from mapping errors. Finally, RES-Scanner can improve the completeness and accuracy of editing site identification when the data of multiple samples are available.<br>RES-Scanner, as a software package written in the Perl programming language, provides a comprehensive solution that addresses read mapping, homozygous genotype calling, de novo RNA-editing site identification and annotation for any species with matching RNA-Seq and DNA-Seq data. The package is freely available at: https://github.com/ZhangLabSZ/RES-Scanner
DOI: 10.5524/100212
title: Supporting data for "High-quality genome assembly of channel catfish, Ictalurus punctatus"

description: The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish species in the world and in the United States aquaculture industry. Since its introduction into China in 1984, both cultivation area and yield of this species has dramatically increased such that China is now by far the leading producer of channel catfish. To aid genomic research into this species, data sets such as genetic linkage groups, long-insert libraries, physical maps, bacterial artificial clones (BAC) end sequences (BES), transcriptome assemblies, and reference genome sequences have been generated. Here, using diverse assembly methods, we provide a comparable high quality genome assembly for a channel catfish from breeding stock inbred in China for more than three generations, which was originally imported to China from North America.<br> Approximately 201.6 gigabases (Gb) of genome reads were sequenced by the Illumina HiSeq 2500 platform. Subsequently, we generated high quality, cost-effective and easily assembled sequences of the channel catfish genome with a scaffold N50 of 7.2 Mb and 95.6% completeness. We also predicted that the channel catfish genome contains 21 556 protein-coding genes and 275.3 millionbases (Mb) of repetitive sequences. <br>We report a high quality genome assembly of the channel catfish, which is comparable to a recent report of the Coco channel catfish. The genome data generated could be used as an initial platform for molecular breeding to obtain novel catfish varieties using genomic approaches.
DOI: 10.5524/100213
title: Gene mapping data of nine agronomic traits and genome assembly data of a foxtail millet RIL population

description: Foxtail millet (Setaria italica) provides food and fodder in semi-arid regions and infertile land. Resequencing of 184 foxtail millet recombinant inbred lines (RILs) was performed to aid the research on species improvement. Bin map were constructed based on the RILs recombination data. By anchoring some unseated scaffolds and filling gap, we update two original millet reference genomes Zhanggu and Yugu to the second edition. Gene mapping of nine agronomic traits were done based on this RIL population. The genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding. Resequencing of the RILs could also provide an effective way for high quantity genome assembly and gene identification.
DOI: 10.5524/100217
title: Advancing open science through NiData

description: The goal of this project is to improve accessibility of open datasets by curating them. NiData aims to provide a common interface for documentation, downloads, and examples to all open neuroimaging datasets, making data usable for experts and non-experts alike. <br>NiData is a Python package that provides a single interface accessing data from a variety of open data sources. The software framework makes it easy to add new data sources, simple to define and to provide access to multiple datasets from a single data source. Software dependencies are managed on a per-dataset basis, allowing downloads and examples to use any public packages without requiring installation of packages required by unused datasets. The interface also allows selective download of data (by subject or type) and caches files locally, allowing easy management of big datasets. <br>We focused on exposing new methods for downloading data from the HCP, supporting access via Amazon S3 and HTTP/XNAT. We were able to provide a downloader that accepts login credentials and downloads files locally. We created an example that interacts with DIPY to produce diffusion imaging results on a single subject from the HCP. We also worked at collecting common data sources, as well as individual datasets stored at each data source, into NiDatas data sources wiki page. We incorporated downloads, documentation, and examples from the nilearn package and began discussion of making a more extensible object model.
DOI: 10.5524/100240
title: Supporting data for “The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization”

description: Nacre, the iridescent material found in pearls and shells of molluscs, is formed through an extraordinary process of matrix-assisted biomineralization. Despite recent advances, many parts of the biomineralization process and its evolutionary origin remain a mystery. The pearl oyster Pinctada fucata martensii is a well-known master of biomineralization, but the molecular mechanisms underlie its production of remarkable shells and pearls is not fully understood.
We sequenced the highly polymorphic genome of the pearl oyster and conducted multi-omic and biochemical studies to probe nacre formation. We identified a large set of novel proteins participating in matrix-framework formation, many in expanded families, including components similar to that found in vertebrate bones such as collagen-related VWA-containing proteins (VWAP), fibronectin, chondroitin sulfotransferases and regulatory elements. 
Considering that there are only collagen-based matrices in vertebrate bones and chitin-based matrices in most invertebrate skeletons, the presence of both chitin and elements of collagen-based matrices in nacre matrices suggests that elements of chitin- and collagen-based matrices are deeply rooted and might be part of an ancient biomineralizing matrix. Our results expand the current shell matrix-framework model and provide new insights into the evolution of diverse biomineralization systems.
DOI: 10.5524/100244
title: Supporting data for "Circadian rhythms have significant effects on leaf-to-canopy scale gas exchange under field conditions"

description: Molecular clocks drive oscillations in leaf photosynthesis, stomatal conductance and other cell and leaf level processes over ~24 h under controlled laboratory conditions. The influence of such circadian regulation over whole-canopy fluxes remains uncertain and diurnal CO2 and H2O vapor flux dynamics in the field are currently interpreted as resulting almost exclusively from direct physiological responses to variations in light, temperature and other environmental factors. We tested whether circadian regulation would affect plant and canopy gas exchange at the Montpellier European CNRS Ecotron. Canopy and leaf level fluxes were constantly monitored under field-like environmental conditions, and under constant environmental conditions (no variation in temperature, radiation or other environmental cues).<br>
We show direct experimental evidence at canopy scales of circadian regulation of daytime gas exchange: 20-79% of the daily variation range in CO2 and H2O fluxes occurred under circadian entrainment in canopies of an annual herb (bean) and of a perennial shrub (cotton). We also observed that considering circadian regulation improved performance by 8-17% in commonly used stomatal conductance models.<br> 
Our results show that circadian controls affect diurnal patterns of CO2 and H2O fluxes in entire canopies in field-like conditions and its consideration significantly improves model performance. Circadian controls act as a memory of the past conditions experienced by the plant that synchronizes metabolism across entire plant canopies.<br>
DOI: 10.5524/100255
title: Supporting data for "Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera)"

description: Sogatella furcifera is an important phloem sap-sucking and plant virus-transmitting migratory insect of rice. Because of its high reproductive potential, dispersal capability and transmission of plant viral diseases, S. furcifera causes considerable damage to rice grain production and has great economical and agricultural impacts. 
Here we present a total of 241.3 Gb of raw reads from the whole genome of S. furcifera generated by Illumina sequencing using different combinations of mate-pair and paired-end libraries from 17 insert libraries ranging between 180 bp and 40 kbp. The final genome assembly (0.72 Gb), with average N50 contig size of 70.7 kb and scaffold N50 of 1.18 Mb, covers 98.6% of the estimated genome size of S. furcifera. Genome annotation, assisted by eight different developmental stages (embryos, 1st-5th instar nymphs, 5-day-old adults and 10-day-old adults), generated 21 254 protein-coding genes, which captured 99.59% (247/248) of core CEGMA genes and 91.7% (2453/2675) of BUSCO genes.<br>
This dataset includes the final genome assemblye of Sogatella furcifera, annotation of the predicted coding genes, peptide translation of predicted coding genes, and annotation of repeat regions within the genome assembly.
DOI: 10.5524/100208
title: Supporting data for "INC-Seq: accurate single molecule reads using nanopore sequencing"

description: Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read error rates (&gt;10%), including RNA-seq, haplotype sequencing and 16S sequencing.
We developed the Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) as a strategy for obtaining long and accurate nanopore reads, starting with low input DNA. Applying INC-Seq for 16S rRNA-based bacterial profiling generated full-length amplicon sequences with a median accuracy &gt;97%.
INC-Seq reads enabled accurate species-level classification, identification of species at 0.1% abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.
DOI: 10.5524/100209
title: De novo sequencing of <i>Ginkgo biloba</i>

description: <em>Ginkgo biloba</em> is one of the worlds most ancient plants, a living fossil that has remained essentially unchanged in terms of gross morphology for more than 200 million years. Representing one of the four extant gymnosperm lineages and having no living relatives, it possesses a suite of fascinating characteristics including including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution.
<br>
Here, we assembled and annotated the first complete genome sequence of ginkgo, which will will aid related research. Genomic DNA was extracted from endosperm tissue from ginkgo seeds that develop directly from female gametophytes without fertilization and thus contain haploid genomes without undergoing genetic recombination. Multiple seeds at visually different developmental stages were collected from five separate large ginkgo trees at one of the ginkgo refuge populations located on Tianmu Mountain, Zhejiang Province, China. All paired-end libraries and one mate-pair library (2 kb) were constructed using DNA extracted from a single seed. Data were generated using a Hiseq 2000/4000 platform from 1253.09 Gb clean data. The resulting assembled 10.61 Gb genome sequence contained 41,840 annotated genes, with N50 values of 48.2 kb for contigs and 1.36 Mb for scaffolds, respectively. Repetitive sequences account for 76.58 % of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent.