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Year 2015, 15 minute measurements of stage, water temperature in a small headwater stream draining a mainly wetland catchment (49% wetlands/swamp + 36% forest), Bear Meadow Brook, draining Cedar Swamp, Reading, MA.
Year 2015, continuous measurements, every 15 minutes, were made of stage and water temperature in a small headwater stream, Bear Meadow Brook , Cedar Swamp, Reading MA, draining a mainly wetland catchment (49% wetland + 36% wetland). Discharge is determined from stage using discharge vs stage regressions.
PIE LTER year 2012, 5 minute and 15 minute measurements of conductivity, water temperature in a small headwater stream draining a mainly wetland catchment (49% wetlands/swamp + 36% forest), Bear Br., draining Cedar Swamp, Reading, MA.
Year 2012, continuous measurements, every 5 minutes during the first deployment and then 15 minutes for the remainder of the year, were made of conductivity, water temperature in Bear Brook in Reading, MA, a small headwater stream draining Cedar Swamp, a mainly wetland catchment (49% wetlands and swamp + 36% forest) in the Ipswich River watershed.
PIE LTER year 2013, 15 minute measurements of conductivity, water temperature in a small headwater stream draining a mainly wetland catchment (49% wetlands/swamp + 36% forest), Bear Br., draining Cedar Swamp, Reading, MA.
Year 2013, continuous measurements, every 15 minutes were made of conductivity, water temperature in Bear Brook in Reading, MA, a small headwater stream draining Cedar Swamp, a mainly wetland catchment (49% wetlands and swamp + 36% forest) in the Ipswich River watershed.
PIE LTER year 2015, 15 minute measurements of conductivity, water temperature in a small headwater stream draining a mainly wetland catchment (49% wetlands/swamp + 36% forest), Bear Br., draining Cedar Swamp, Reading, MA.
Year 2015, continuous measurements, every 15 minutes were made of conductivity, water temperature in Bear Brook in Reading, MA, a small headwater stream draining Cedar Swamp, a mainly wetland catchment (49% wetlands and swamp + 36% forest) in the Ipswich River watershed.
PIE LTER year 2014, 15 minute measurements of conductivity, water temperature in a small headwater stream draining a mainly wetland catchment (49% wetlands/swamp + 36% forest), Bear Br., draining Cedar Swamp, Reading, MA.
Year 2014, continuous measurements, every 15 minutes were made of conductivity, water temperature in Bear Brook in Reading, MA, a small headwater stream draining Cedar Swamp, a mainly wetland catchment (49% wetlands and swamp + 36% forest) in the Ipswich River watershed.
Raw Nanopore data for "Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia, and Genomic Insights into 4-Aminobenzenesulfonate, p-Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga"
<p>This is the raw Nanopore dataset (fast5) for Hydrogenophaga intermedia PBC. The gDNA was prepared using the now obsolete SQK-NSK007 kit and sequenced on a MINION R9 Flowcell. </p>
Chloroplast genome sequencing reads from snow gum
<p>Tutorial data for chloroplast genome assembly: fastq reads from illumina and nanopore sequencing for the snow gum, <em>Eucalyptus pauciflora</em>.</p> <p>Data from: Wang, W., Schalamun, M., Morales-Suarez, A. et al. Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics 19, 977 (2018) doi:10.1186/s12864-018-5348-8</p> <p>Data hosted at NCBI under accession numbers: illumina (SRR7153063) and nanopore (SRR7153095). Additional illumina file SRR7153071 not used here. </p> <p>This is how the files have been changed from the original datasets: </p> <p>Using the Galaxy platform (usegalaxy.org): </p> <ul> <li> <p>Each dataset was separately mapped to the NCBI Reference Sequence for <em>Eucalyptus pauciflora </em>chloroplast NC_039597.1, using BWA-MEM. </p> </li> <li> <p>Unmapped reads were filtered out using a SAMtools flag. </p> </li> <li> <p>Bam files were converted to fastq files.</p> </li> <li> <p>Each fastq file was then reduced in size:</p> </li> <li> <p>snow-gum-illumina-cp-reduced: has the first 62,500 reads only. Note that original pairing of reads has not been preserved so consider these to be unpaired reads for this tutorial.</p> </li> <li> <p>snow-gum-nanopore-cp-reduced: has only reads that are longer than 90,000 bp.</p> </li> </ul>
Dataset for "Nanopore-led long-read genome assembly of the Australian yabby, Cherax destructor"
<p>Intermediate_Assemblies.tar.gz: Intermediate genome assemblies e.g. raw wtdbg assembly (CD.raw.fa), polished wtdbg assembly (CD.cns.fa), 1st pilon polished assembly (CDF2_pilon1.fasta), 2nd pilon polished assembly (CDF2_pilon2.fasta) and RNA-scaffolded assembly (CDF2_pilon2_prna.fasta). Folders with run_"assembly name" are BUSCO output for each of the assembly.</p> <p>BRAKER2.tar.gz: BRAKER2 genome annotation output containing the initial set of predicted protein-coding genes as well as training intermediate files.</p> <p>BUSCOv3.tar.gz: BUSCO assessment of publicly available Decapod crustacean genome assemblies</p> <p>Cdes.filtered.codingseq: Filtered set of protein-coding sequences</p> <p>Cdes.filtered.faa: Translation of the filtered protein-coding sequences</p> <p>CDF2.NCBI.fasta.masked.gz: Repeat-masked (softmasked) Cherax destructor genome</p> <p>Cqua_transcriptome.tar.gz: rnaSPAdes output (combined fasta) of all Cherax quadricarinatus transcriptomes and its reduced dataset generated by EvidentialGene. </p> <p>Quast.tar.gz: Quast output of all Decapod crustacean genome assemblies assessed in this study</p> <p>Repeat_Annotation.tar.gz: Repeat annotation (.gff3) based on Cherax destructor-specific de novo repeat library and its summary (.tbl)</p> <p>RepeatLibrary.tar.gz: Cherax destructor-specific de novo repeat library generated by RepeatModeler</p> <p>Wtdbg2_assembly.log: Wtdbg2.5 log file showing exact command used, kmer distribution, memory usage and assembly duration.</p> <p>CAZY_Annotation.tar.gz: dbCAN2 Identification of CAZy in the selected crustacean proteomes as well as list of cellulase-associated GH groups (glycoside hydrolase). </p> <p>Orthofinder.tar.gz: Orthofinder2 output and proteomes of each crustacean used to infer orthologous clustering.</p> <p>GH9_Analysis.tar.gz: Selected GH9-associated protein sequences, amino acid alignment and IQTree output. </p> <p>Cdes_mito.gbf: GenBank file of the annotated complete mitogenome</p> <p>Cdes.filtered.codingseq: Cherax destructor protein-coding genes with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p> <p>Cdes.filtered.faa: Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p> <p>Cdes.ortholog.list: List of predicted Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p>
Experimental data for "Virtual Reality as a Tool for Promoting Reading via Enhanced Narrative Absorption and Empathy"
<p>This dataset contains data of the publication "Virtual Reality as a Tool for Promoting Reading via Enhanced Narrative Absorption and Empathy". It includes measure for the Story World Absorption Scale and the State Empathy Scale used to compare subjective experiences while reading on paper and reading in a virtual reality environment.</p> <p>Original paper: Pianzola, F., Bálint, K., and Weller, J. (2019). Virtual Reality as a Tool for Promoting Reading via Enhanced Narrative Absorption and Empathy. <em>Scientific Study of Literature 9</em>(2). https://doi.org/10.1075/ssol.19013.pia</p>
Training data for 'Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads' tutorial (Galaxy Training Material)
<p>The data here is a copy of the corresponding SRR records in the NCBI SRA. The duplication serves a dual purpose:</p> <ol> <li>as a backup should there be problems connecting to NCBI servers, e.g., during Galaxy user trainings.</li> <li>to illustrate how to obtain raw sequencing data from alternative sources, and to organize the data into the same collection structure in a Galaxy history that is generated by specialized Galaxy SRA download tools.</li> </ol>
Pangeo Cloud Storage Read Throughput Benchmarks
<p>These are the results of benchmarking distributed reads from various cloud storage services and data formats. All tests were performed from the Google cloud US-CENTRAL1 region.</p>
Data from: Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription
<p>One of the widely used applications of the popular Cre-loxP method for targeted recombination is the permanent activation of marker genes, such as reporter genes or antibiotic resistance genes, by excision of a preceding transcriptional stop signal. The STOP cassette consists of three identical SV40-derived poly(A) signal repeats and is flanked by two loxP sites. We found that in addition to complete loxP-mediated recombination, limiting levels of the Cre recombinase also cause incomplete recombination of the STOP cassette. Partial recombination leads to the loss of only one or two of the three identical poly(A) repeats with recombination breakpoints always precisely matching the end/start of each poly(A) signal repeat without any relevant similarity to the canonical or known cryptic loxP sequences, suggesting that this type of Cre-mediated recombination is loxP-independent. Incomplete deletion of the STOP cassette results in partial read-through transcription, explaining at least some of the variability often observed in marker gene expression from an otherwise identical locus.</p>
Speed up your close-reading -- EviDENce
<p><strong>The EviDENce Framework tool</strong></p> <p>Even in the era of digitized collections, scholarly interaction with source materials – i.e. close reading – remains a key element of humanities research, while standard digital query methods are often perceived as restrictive.</p> <p> </p> <p>The EviDENce corpus creation framework provides scholars with a tool to intuitively interact with a collection, starting from manually selected elements and employing abstract high level similarity measures to suggest further relevant source material for further inspection – </p> <p> </p> <p><strong>Efficient close reading with machine-learning support</strong></p> <p><strong>----------</strong></p> <p>This video demonstrates the capabilities and use of the EviDENce framework tool</p>
Anonumous Dataset of PAYT readings used for Waste4Think papers. Data used for the following publication: https://zenodo.org/record/3532968#.XvMgz-dS-w6
<p>This dataset is the anonymous version of the full confidential dataset related to individual waste bag generation monitoring through RFID in Seveso, used for Pay As You Throw invoicing.</p> <p>Summary statistics and charts are included in the Excel, and used to prepare the related article</p>
Next-generation sequencing of newborn screening genes: The accuracy of short-read mapping
<p>We examine the effect of high homology genomic regions on the mapping of genes related to newborn screening while taking different read lengths and patient's ethnic background into consideration.</p>
Dataset for "Learning to Read and Follow Music in Complete Score Sheet Images"
<p>This is the data used in the paper:<br> Florian Henkel , Rainer Kelz, Gerhard Widmer. "Learning to Read and Follow Music in Complete Score Sheet Images". Proceedings of the 21st International Society for Music Information Retrieval Conference (ISMIR), 2020</p> <p>The dataset is based on the <a href="https://zenodo.org/record/2597505#.XxbJtxGxVhE">MSMD - Multimodal Sheet Music Dataset</a> and processed for the purpose of score following in complete score sheet images.</p> <pre>Please find further information and the corresponding code on this Github page: <a href="https://github.com/CPJKU/audio_conditioned_unet">https://github.com/CPJKU/audio_conditioned_unet</a> </pre>
Consensus calling of MinION amplicon reads improves metabarcoding results
<p><strong>Background</strong>: Metabarcoding environmental DNA with high-throughput sequencing is a state-of-the-art method to assess biodiversity and to uncover dark taxa. MinION is the first handheld sequencer that can be taken into the field for on-site metabarcoding. This research aims to answer if bioinformatics can solve the issues that arise because of the higher error rate of MinION data.</p> <p><strong>Results</strong>: Biodiverse samples with a presumed large portion of dark taxa were selected from the Dutch Caribbean. The cytochrome oxidase 1 gene (CO1) is used as a barcode for identification at the species level or higher levels. Generating a consensus sequence from closely related sequences resulted in minimized random errors and increased species identification of 175% compared to unclustered MinION data. Additional to the formulation of the workflow, an ecological analysis was conducted that revealed co-occurrence of species in similar habitats, and that the proportion of dark taxa in the sampled region is 81.87%.</p> <p><strong>Conclusion</strong>: Although the workflow did not attain the results that the existing Illumina workflows do, the potential is evident. The high proportion of dark taxa in the sampled region of Statia and the Saba Bank indicates the need for continued barcoding of species in the Dutch Caribbean to resolve database limitations.</p>
The Marginal Latin (LaM) readings of 2 Samuel - all the cases collected
<p>Collected textual cases for my SBL 2020 paper "The Marginal Latin (LaM) readings of 2 Samuel".</p>
Reads brutas - Sequenciamento de glândula de veneno de Viuva Negra
<p>Reads brutas obtidas a partir do sequenciamento de glândula de veneno de Viuva Negra. Quantificação dos transcritos adicionada também.</p>
Koranic Science Readings of NÂFI' [IO Bijapur 274]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Bijapur 274 in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 45 here with further notations and hyperlinks]</strong>.</li> </ul> <p>45.</p> <p>B 274. Size 7 in. by 5 in.; foll. 58. Nineteen lines in a page.</p> <ol> <li> <p>(foll. 16-49). A treatise on the Readings of NÂFI’, as handed down by his two pupils Ḳâlûn and Warsh; derived from SHÂṬIBÎ.</p> </li> </ol> <p>Beginning: الحمدلله الذی فتح علینا ابواب العرفان ....و بعد فهذه رسالة فی بیان قراءة الامام البارع الحافظ الثقة امام نافع المدنی رضه بروایة الامامین قالون وورش علی ما رواه الامام الهمام ولی الله ابوالقاسم الشاطبی رضه.</p> <p>In two chapters: the first treating of the general principles of Nâfi’ (الاصول), and the other giving a detailed account of his Readings, following the order of the Sûrahs (فی فرش الحروف). Preceded by an introduction on technical terms: مقدّمة فی بیان اصطلاحات اهل القراءة.</p> <ol> <li> <p>(foll. 50-58). A list of passages or words of the Koran (styled حرف), according to the order of the Sûrahs, the purpose of which is not indicated.</p> </li> </ol> <p>There is no preface. Beginning, after the Basmalah:</p> <p>سورة البقرة فیه هدی قیل لهم لا تفسدو.</p> <p>Plainly written. Inscribed in a later hand: رساله عجیبه.</p> <p>There precedes a fragment of a <em>Persian</em> treatise on the Reading of the Koran.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.