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2,848 results for “sequence data”
FIGURE 32 Occulta ocnus comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 32 Occulta ocnus comb.n. Locality records.
FIGURE 29 Trico tricolor comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 29 Trico tricolor comb.n. Locality records.
FIGURE 25 Xenovena murrayae comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 25 Xenovena murrayae comb.n. Locality records.
FIGURE 22 Taguaiba gen.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 22 Taguaiba gen.n. Species diversity mapped on a 2 degree grid.
RAD2-065 Erenna sp. sequence data
<p>RNAseq and genome assembly data for the siphonophore Erenna sp.</p> <p>Files:</p> <p>RAD2-065_ISOseq_clustered.hq.fasta --> PacBio IsoSeq mRNA assembly file</p> <p>RAD2-065.clustered.hq.fasta.transdecoder.pep --> translated proteins from the transcriptome. Includes annotation information from swissprot and pfam.</p> <p>RAD2-065_primary.genome.scf_m1000.fasta --> combined genome assembly. NOTE: only covers a small fraction of the estimated genome of >27Gbp. Contains few genes. Submitted for reference.</p>
Data Repository - Impact of competing energy scales on the shell-filling sequence in elliptic bilayer graphene quantum dots
<p>Data Repository for the Publication: Impact of competing energy scales on the shell-filling sequence in elliptic bilayer graphene quantum dots</p> <p>Abstract:</p> <p>We report on a detailed investigation of the shell-filling sequence in electrostatically defined elliptic bilayer graphene quantum dots (QDs) in the regime of low charge carrier occupation, N < 12, by means of magnetotransport spectroscopy and numerical calculations. We show the necessity of including both short-range electron-electron interaction and wavefunction-dependent valley g-factors for understanding the overall fourfold shell-filling sequence. These factors lead to an additional energy splitting at half-filling of each orbital state and different energy shifts in out-of-plane magnetic fields. Analysis of 31 different BLG QDs reveals that both valley g-factor and electron-electron interaction induced energy splitting increase with decreasing QD size, validating theory. However, we find that the electrostatic charging energy of such gate-defined QDs does not correlate consistently with their size, indicating complex electrostatics. These findings offer significant insights for future BLG QD devices and circuit designs.</p>
12S eDNA sequence data from a Maldivian Coral reef
<p>Raw eDNA sequence data and meta (including the tag files) data for the study of a coral reef in the Maldives.</p> <p>Used in the study: Field collections and environmental DNA surveys reveal topographic complexity of coral reefs as a predictor of cryptobenthic biodiversity across small spatial scales</p> <p> </p>
Raw sequence data for epiphytic fungi in an alpine grassland
<p>A field investigation for plant surface microbes of two dominant grassland species were conducted through 18S rRNA sequencing</p>
Data and code for, "Large language models design sequence-defined macromolecules via evolutionary optimization"
<div> <pre># Codes and data for "Large language models design sequence-defined macromolecules via evolutionary optimization"<br><br>Note this repository contains codes and data files for the manuscript. This is a snapshot of the repository, frozen at the time of submission.<br><br># Codes<br><br>## LLM codes<br>- `run_claude.py` - the routine for performing LLM-based rollouts; intended for command line execution using argparse<br>- `message_utils.py` - utilities for constructing and parsing messages for LLM I/O<br>- `model_utils.py` - lightweight utilities for retrieving formatted predictions from the RNN ensemble<br>- `target_defs.py` - defines the sequence, locations, and natural language descriptions of the target structures<br>- `ask_about_oracle.ipynb` - asks the LLM to speculate about the nature of the optimization task<br><br>## other algorithms<br>- `active_learning.ipynb` - use EI acquisition with RF surrogate to label new sequences; includes an unused tokenization scheme<br>- `evolutionary_algorithm.ipynb` - use DEAP library to perform evolutionary optimization<br>- `random_sampling.ipynb` - sample sequences randomly from all possible sequences<br><br>## postprocessing<br>- `process_aggregated_logs.py` - reads data from the raw log files and prepares them for visualization<br>- `process_sample_rollouts.py` - reads data from the raw log files and prepares individual rollouts<br><br>## visualization<br>- `figure1b.ipynb` - renders panel b of Fig. 1<br>- `figure1efg.ipynb` - renders the last row of Fig. 1 (panels e-g)<br>- `figure2.ipynb` - renders all of Fig. 2<br>- `figure_si.ipynb` - renders Figs. S1 and S2<br>- `figure_md_validation.ipynb` - renders Fig. S3<br><br># Data files<br><br>- `prompts/`<br> - `prompt-scientific-v4.4.yml` - the full text of the scientific prompt, to be read by `run_claude.py`<br> - `prompt-oracle-v4.4.yml` - the full text of the oracle prompt, to be read by `run_claude.py`<br>- `models/` - the TorchScript RNN models used to make predictions<br>- `data/`<br> - `embeddings` - calculated embeddings for a collection of sequences from our prior work<br> - `llm-logs` - the raw logs obtained from the Claude 3.5 Sonnet LLM (other algorithms made to look like the LLM logs after the fact)<br> - `llm-logs-opus` - the raw logs obtained from the Claude 3.0 Opus LLM (used in the first draft of the article, replaced by Claude 3.5 Sonnet) <br> - `all-rollouts-kltd.csv` - postprocessed logs for all the rollouts using the "top $k < d^*$" metric<br> - `all-rollouts-topkd.csv` - postprocessed logs for all the rollouts using the "mean $d$ for top $k$" metric<br> - `sample-rollout-membranes-x-3.csv` - postprocessed logs for a single rollout replica, `x` = each algorithm type<br> - `snapshots` - png snapshots of MD simulation results at different locations in the manifold</pre> </div>
Real-world Therapy of ALK-positive NSCLC in Sweden: the Sequencing of ALK Tyrosine Kinase Inhibitor Drugs and Their Therapeutic Outcomes Based on Data From National Registers.
ClinicalTrials.gov study NCT04647110. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum
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Data from: Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii
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Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data
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Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species
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Oxylobus (Asteraceae) analysis DNA sequence data
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Data from: Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences
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Data from: Genome-wide identification of microsatellites and transposable elements in the dromedary camel genome using whole genome sequencing data
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Data from: De novo sequencing, assembly, and annotation of four threespine stickleback genomes based on microfluidic partitioned DNA libraries
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Data from: "Development of the draft genome sequence of the marbled flounder Pseudopleuronectes yokohamae as a reference of population genomic analysis" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015
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Data from: Intraspecific trait variation and colonization sequence alter community assembly and disease epidemics
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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)
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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.