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zenodo32/100

Evaluation of global forcing data sets for hydropower inflow simulation in Nepal

We are thankful to the Department of Hydrology and Meteorology, Government of Nepal for providing observed hydrological and Meteorological data sets for this study. Some of the data presented here are subject of copyright so we request to contact author (corresponding author: bikasbhattarai@gmail.com) for further use for publication.

opencc-by-4.0Dec 2019View details →

zenodo32/100

Microsoft Academic data set for RPYS analysis

Microsoft Academic data set for RPYS analysis, used in "Discovering seminal works with marker papers", see https://arxiv.org/abs/1901.07352 Please see also: https://aka.ms/msracad Arnab Sinha, Zhihong Shen, Yang Song, Hao Ma, Darrin Eide, Bo-June (Paul) Hsu, and Kuansan Wang. 2015. An Overview of Microsoft Academic Service (MA) and Applications. In Proceedings of the 24th International Conference on World Wide Web (WWW '15 Companion). ACM, New York, NY, USA, 243-246. DOI=http://dx.doi.org/10.1145/2740908.2742839

openodc-byDec 2019View details →

zenodo32/100

Internal Wave Bolus Data Set

Image files for experiments of internal wave boluses.  Stratification data for the experiments is also included.

opencc-by-4.0Jan 2020View details →

zenodo32/100

Data set: Grain Reynolds number scale effects in dry granular slides

Scale series of velocity, flow depth and run out data for dry granular materials flowing down a slope with side walls.

opencc-by-4.0Jan 2020View details →

zenodo32/100

mOTUs 1.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: mOTUs SoftwareVersion: 1.1 DataURL: https://data.cami-challenge.org/participate SoftwareURL: http://www.bork.embl.de/software/mOTUs1/ DockerImage: stefanjanssen/docker_profiling_tools:motu IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: mOTU.v1.padded ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:motu

opencc-by-4.0Jan 2020View details →

zenodo32/100

FOCUS 0.31 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: FOCUS SoftwareVersion: 0.31 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/metageni/FOCUS DockerImage: stefanjanssen/docker_profiling_tools:focus IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: k8_bacterial_and_draft ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:focus

opencc-by-4.0Jan 2020View details →

zenodo32/100

MetaPhlAn 2.9.21 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: MetaPhlAn SoftwareVersion: 2.9.21 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://bitbucket.org/biobakery/metaphlan2 DockerImage: cami/metaphlan:2.9.21 IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: mpa_v29_CHOCOPhlAn_201901 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ --volume="/path/to/reference_database:/exchange/db:rw" \ cami/metaphlan:2.9.21

opencc-by-4.0Jan 2020View details →

zenodo32/100

MetaPhlAn 2.2.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: MetaPhlAn SoftwareVersion: 2.2.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://bitbucket.org/biobakery/metaphlan2 DockerImage: stefanjanssen/docker_profiling_tools:metaphlan2 IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: mpa_v20_m200 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:metaphlan2

opencc-by-4.0Jan 2020View details →

zenodo32/100

CAMIARKQuikr 1.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: CAMIARKQuikr SoftwareVersion: 1.0.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://doi.org/10.5281/zenodo.1730572 DockerImage: stefanjanssen/docker_profiling_tools:quickr IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: https://doi.org/10.5281/zenodo.1730572 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:quickr

opencc-by-4.0Jan 2020View details →

zenodo32/100

DAS Tool 1.1.2 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly. Refinement of the binning output of MaxBin 2.2.7, MetaBAT 2.12.1, CONCOCT 1.0.0, and DAS Tool 1.1.2. Software: DAS Tool SoftwareVersion: 1.1.2 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/cmks/DAS_Tool DockerImage: cami/das_tool:1.1.2 IsBiobox: No ShortReadsUsed: True LongReadsUsed: False CommandUsed: DAS_Tool -i binning_concoct1.0.0,binning_maxbin2.2.7,binning_metabat2.12.1 -c anonymous_gsa_pooled.fasta -o output --search_engine diamond

opencc-by-4.0Jan 2020View details →

zenodo32/100

CONCOCT 1.0.0 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly Software: CONCOCT SoftwareVersion: 1.0.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/BinPro/CONCOCT DockerImage: quay.io/biocontainers/concoct:1.0.0--py37h88e4a8a_5 IsBiobox: No ShortReadsUsed: True LongReadsUsed: False CommandUsed: for i in {0..63}; do bowtie2 -q --threads 30 --fr -x anonymous_gsa_pooled.fasta --interleaved sample_${i}/anonymous_reads.fq -S anonymous_reads_sample_${i}.sam ; done for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done cut_up_fasta.py anonymous_gsa_pooled.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa concoct_coverage_table.py contigs_10K.bed /host/benchmarking/fmeyer/output/bowtie2/mouse_gut/sorted_bam/anonymous_reads_sample_*.sorted.bam > coverage_table.tsv concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b merge_cutup_clustering.py clustering_gt1000.csv > clustering_merged.csv

opencc-by-4.0Jan 2020View details →

zenodo32/100

MEGAN 6.15.2 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: MEGAN SoftwareVersion: 6.15.2 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/husonlab/megan-ce ReferenceDatabase: NCBI nr 2019-04-17 Taxonomy: NCBI 2019-04-17 ShortReadsUsed: False LongReadsUsed: False CommandUsed: diamond makedb --in nr.faa.gz --db nr_diamond0.9.24 --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp diamond blastx -d nr_diamond0.9.24 -q anonymous_gsa_pooled.fasta -a result -t tmp --index-chunks 1 megan/tools/daa2rma -i result.daa -o 19122017_mousegut_scaffolds.rma --acc2taxa megan/prot_acc2tax-Nov2018X1.abin #final bins extracted with MEGAN's graphical interface tool

opencc-by-4.0Jan 2020View details →

zenodo32/100

MetaPhyler 1.25 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: MetaPhyler SoftwareVersion: 1.25 DataURL: https://data.cami-challenge.org/participate SoftwareURL: http://metaphyler.cbcb.umd.edu/ DockerImage: stefanjanssen/docker_profiling_tools:metaphyler IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: 2012 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:metaphyler

opencc-by-4.0Jan 2020View details →

zenodo32/100

DIAMOND 0.9.24 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: DIAMOND SoftwareVersion: 0.9.24 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/bbuchfink/diamond ReferenceDatabase: NCBI nr 2019-04-17 Taxonomy: NCBI 2019-04-17 ShortReadsUsed: False LongReadsUsed: False CommandUsed: diamond makedb --in nr.faa.gz --db nr --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp diamond blastx --query anonymous_gsa_pooled.fasta --db nr --outfmt 102 --out 19122017_mousegut_scaffolds.out --block-size 40 --index-chunks 1 --tmpdir tmp

opencc-by-4.0Jan 2020View details →

zenodo32/100

mOTUs 2.5.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: mOTUs SoftwareVersion: 2.5.1 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://motu-tool.org/ DockerImage: cami/motus:2.5.1 IsBiobox: False ReferenceDatabase: mOTUs database version 2.5.0 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: for i in {0..63}; do motus profile -f sample_$((i))/reads/anonymous_reads_r1.fq -r sample_$((i))/reads/anonymous_reads_r2.fq -n $((i)) -C precision > sample$((i)).profile ; done cat sample*.profile > cami2_mouse_gut_motus2.5.1.profile

opencc-by-4.0Jan 2020View details →

zenodo32/100

MaxBin 2.2.7 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly Software: MaxBin SoftwareVersion: 2.2.7 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://sourceforge.net/projects/maxbin/ DockerImage: cami/maxbin:2.2.7 IsBiobox: No ShortReadsUsed: True LongReadsUsed: False CommandUsed: run_MaxBin.pl -thread 16 -contig anonymous_gsa_pooled.fasta -out output -reads sample_0/reads/anonymous_reads.fq -reads2 sample_1/reads/anonymous_reads.fq -reads3 sample_2/reads/anonymous_reads.fq -reads4 sample_3/reads/anonymous_reads.fq -reads5 sample_4/reads/anonymous_reads.fq -reads6 sample_5/reads/anonymous_reads.fq -reads7 sample_6/reads/anonymous_reads.fq -reads8 sample_7/reads/anonymous_reads.fq -reads9 sample_8/reads/anonymous_reads.fq -reads10 sample_9/reads/anonymous_reads.fq -reads11 sample_10/reads/anonymous_reads.fq -reads12 sample_11/reads/anonymous_reads.fq -reads13 sample_12/reads/anonymous_reads.fq -reads14 sample_13/reads/anonymous_reads.fq -reads15 sample_14/reads/anonymous_reads.fq -reads16 sample_15/reads/anonymous_reads.fq -reads17 sample_16/reads/anonymous_reads.fq -reads18 sample_17/reads/anonymous_reads.fq -reads19 sample_18/reads/anonymous_reads.fq -reads20 sample_19/reads/anonymous_reads.fq -reads21 sample_20/reads/anonymous_reads.fq -reads22 sample_21/reads/anonymous_reads.fq -reads23 sample_22/reads/anonymous_reads.fq -reads24 sample_23/reads/anonymous_reads.fq -reads25 sample_24/reads/anonymous_reads.fq -reads26 sample_25/reads/anonymous_reads.fq -reads27 sample_26/reads/anonymous_reads.fq -reads28 sample_27/reads/anonymous_reads.fq -reads29 sample_28/reads/anonymous_reads.fq -reads30 sample_29/reads/anonymous_reads.fq -reads31 sample_30/reads/anonymous_reads.fq -reads32 sample_31/reads/anonymous_reads.fq -reads33 sample_32/reads/anonymous_reads.fq -reads34 sample_33/reads/anonymous_reads.fq -reads35 sample_34/reads/anonymous_reads.fq -reads36 sample_35/reads/anonymous_reads.fq -reads37 sample_36/reads/anonymous_reads.fq -reads38 sample_37/reads/anonymous_reads.fq -reads39 sample_38/reads/anonymous_reads.fq -reads40 sample_39/reads/anonymous_reads.fq -reads41 sample_40/reads/anonymous_reads.fq -reads42 sample_41/reads/anonymous_reads.fq -reads43 sample_42/reads/anonymous_reads.fq -reads44 sample_43/reads/anonymous_reads.fq -reads45 sample_44/reads/anonymous_reads.fq -reads46 sample_45/reads/anonymous_reads.fq -reads47 sample_46/reads/anonymous_reads.fq -reads48 sample_47/reads/anonymous_reads.fq -reads49 sample_48/reads/anonymous_reads.fq -reads50 sample_49/reads/anonymous_reads.fq -reads51 sample_50/reads/anonymous_reads.fq -reads52 sample_51/reads/anonymous_reads.fq -reads53 sample_52/reads/anonymous_reads.fq -reads54 sample_53/reads/anonymous_reads.fq -reads55 sample_54/reads/anonymous_reads.fq -reads56 sample_55/reads/anonymous_reads.fq -reads57 sample_56/reads/anonymous_reads.fq -reads58 sample_57/reads/anonymous_reads.fq -reads59 sample_58/reads/anonymous_reads.fq -reads60 sample_59/reads/anonymous_reads.fq -reads61 sample_60/reads/anonymous_reads.fq -reads62 sample_61/reads/anonymous_reads.fq -reads63 sample_62/reads/anonymous_reads.fq -reads64 sample_63/reads/anonymous_reads.fq

opencc-by-4.0Jan 2020View details →

zenodo32/100

InterFlex WP3 data set for scalability and replicability analysis of InterFlex demonstrators

This set of data includes the data for the scalability and replicability task of InterFlex project under GA 731289 for the functional (grid operation) and ICT conducted analyses of the demonstrated use cases. The results and the detailed report can be found in deliverable D3.8

opencc-by-4.0Jan 2020View details →

zenodo32/100

LogChunks: A Data Set for Build Log Analysis

We collected 797 Travis CI logs from a wide range of 80 GitHub repositories from 29 different main development languages. You can find our collection tool in `log-collection` and the logs sorted by language and repository in `logs`. We manually labeled the part (chunk) of the log describing why the build failed.In addition, the chunks are annotated with keywords that we would use to search for them and categorized according to their structural representation within the log. You can find this data in an xml-file for each repository in `build-failure-reason`.

opencc-by-4.0Jan 2020View details →

zenodo32/100

MEGAHIT 1.0.3, 1.1.3, 1.2.9 assembly of the CAMI 2 Mouse Gut Toy data set, samples 0-9, short reads

Assembly of the first 10 short read samples with different MEGAHIT versions and parameters Software: MEGAHIT SoftwareVersion: 1.0.3, 1.1.3, 1.2.9 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/voutcn/megahit ShortReadsUsed: True LongReadsUsed: False CommandUsed: # install bioconda and run: conda create -n megahit103 megahit=1.0.3 conda create -n megahit113 megahit=1.1.3 conda create -n megahit129 megahit=1.2.9 Sample0=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz Sample1=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz Sample2=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_2/reads/anonymous_reads.fq.gz Sample3=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_3/reads/anonymous_reads.fq.gz Sample4=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_4/reads/anonymous_reads.fq.gz Sample5=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_5/reads/anonymous_reads.fq.gz Sample6=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_6/reads/anonymous_reads.fq.gz Sample7=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_7/reads/anonymous_reads.fq.gz Sample8=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_8/reads/anonymous_reads.fq.gz Sample9=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_9/reads/anonymous_reads.fq.gz conda activate megahit103 /usr/bin/time -v megahit -t 48 \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit103-Sample0-9-sLibs-default conda activate megahit113 /usr/bin/time -v megahit -t 48 \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit113-Sample0-9-sLibs-default /usr/bin/time -v megahit -t 48 --presets meta-sensitive \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit113-Sample0-9-sLibs-meta-sensitive /usr/bin/time -v megahit -t 48 --presets meta-large \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit113-Sample0-9-sLibs-meta-large conda activate megahit129 /usr/bin/time -v megahit -t 48 \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit129-Sample0-9-sLibs-default

opencc-by-4.0Feb 2020View details →

zenodo32/100

metaSPAdes 3.13.0 assembly of the CAMI 2 Mouse Gut Toy data set, samples 0-9, short reads

Assembly of the first 10 short read samples Software: metaSPAdes SoftwareVersion: 3.13.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/ablab/spades ShortReadsUsed: True LongReadsUsed: False CommandUsed: conda create -n spades3130 spades=3.13.0-0 Sample0=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz Sample1=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz Sample2=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_2/reads/anonymous_reads.fq.gz Sample3=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_3/reads/anonymous_reads.fq.gz Sample4=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_4/reads/anonymous_reads.fq.gz Sample5=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_5/reads/anonymous_reads.fq.gz Sample6=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_6/reads/anonymous_reads.fq.gz Sample7=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_7/reads/anonymous_reads.fq.gz Sample8=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_8/reads/anonymous_reads.fq.gz Sample9=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_9/reads/anonymous_reads.fq.gz cat $Sample0 $Sample1 $Sample2 $Sample3 $Sample4 $Sample5 $Sample6 $Sample7 $Sample8 $Sample9 > Samples0-9_anonymous_reads.fq.gz conda activate spades3130 /usr/bin/time -v metaspades.py --12 Samples0-9_anonymous_reads.fq.gz -o metaSPAdes3130-Sample0-9

opencc-by-4.0Feb 2020View details →

ScienceDex guides

Understand access before you commit

These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

Compare curated 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.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record