The Biological Sampling Database (BSD) is an Oracle relational database that is maintained at the NMFS Panama City Laboratory and NOAA NMFS Beaufort Laboratory. Data set includes port samples of reef fish species collected from commercial and recreational fishery landings in the U.S. South Atlantic (NC - FL Keys). The data set serves as an inventory of samples stored at the NMFS Beaufort Laboratory as well as final processed data. Information that may be inlcuded for each sample is trip level information, species, size meansurements, age, sex and reproductive data.

Spreedsheet contains FTIR data of Jackfruit samples stored at refrigerated temperatures

A collection of diverse human biospecimens and their associated clinical and molecular data, available for research purposes through the Specie Bio BioExchange platform. This dataset is contributed by a network of biobanks, academic medical centers, and other research institutions.

Much machine learning research progress is based on developing models and evaluating them on a benchmark dataset (e.g., ImageNet for images). However, applying such benchmark-successful methods to real-world data often does not work as expected. This is particularly the case for biological data where we expect variability at multiple time and spatial scales. Typical benchmark data has simple, dominant semantics, such as a number, an object type, or a word. In contrast, biological samples often have multiple semantic components leading to complex and entangled signals. Complexity is added if the signal of interest is related to atypical states, e.g., disease, and if there is limited data available for learning.In this work, we focus on image classification of real-world biological data that are, indeed, different from standard images. We are using grain data and the goal is to detect diseases and damages, for example, “pink fusarium” and “skinned”. Pink fusarium, skinned grains, and other diseases and damages are key factors in setting the price of grains or excluding dangerous grains from food production. Apart from challenges stemming from differences of the data from the standard toy datasets, we also present challenges that need to be overcome when explaining deep learning models. For example, explainability methods have many hyperparameters that can give different results, and the ones published in the papers do not work on dissimilar images. Other challenges are more general: problems with visualization of the explanations and their comparison since the magnitudes of their values differ from method to method. An open fundamental question also is: How to evaluate explanations? It is a non-trivial task because the “ground truth” is usually missing or ill-defined. Also, human annotators may create what they think is an explanation of the task at hand, yet the machine learning model might solve it in a different and perhaps counter-intuitive way. We discuss several of these challenges and evaluate various post-hoc explainability methods on grain data. We focus on robustness, quality of explanations, and similarity to particular “ground truth” annotations made by experts. The goal is to find the methods that overall perform well and could be used in this challenging task. We hope that the proposed pipeline would be used as a framework for evaluating explainability methods in specific use cases.

In the later part of 1999, a relational Microsoft Access database was created to accommodate a wide range of data on the phytoplankton Karenia brevis. This database, termed HAB Historical Database (HHD), was designed to efficiently capture core information, yet have the capacity to expand and capture related sampling information if it is available. It performs this task through a series of connected data tables and related forms. The minimum parameters required in order for a sample record to be entered into the database are a K. brevis count (in cells per liter), the date when the water sample was collected, and a description of where the water sample was taken. Datasheets that contained these minimum requirements were compiled from various investigative cruise projects, and state, county, and private agencies, which had collected samples that contained K. brevis. These datasheets varied greatly in specificity of information from the minimum required parameters to detailed cruise and research studies. Due to this diversity, it was decided to incorporate as many entry fields as possible for related information from the datasheet.

The "Protein Data Bank (PDB) archive" was established in 1971 as the first open-access digital data archive in biology. It is a collection of three-dimensional (3D) atomic-level structures of biological macromolecules (i.e., proteins, DNA, and RNA) and their complexes with one another and various small-molecule ligands (e.g., US FDA approved drugs, enzyme co-factors). For each PDB entry (unique identifier: 1abc or PDB_0000001abc) multiple data files contain information about the 3D atomic coordinates, sequences of biological macromolecules, information about any small molecules/ligands present in the entry, details about the structure-determination experiment, authors and publication information, experimental data, and the wwPDB validation report. Additional content stored in the archive includes documentation, summary reports, and software (among others). The PDB is a jointly-managed core archive of the Worldwide Protein Data Bank partnership [RCSB Protein Data Bank (RCSB PDB, rcsb.org); Protein Data Bank in Europe (PDBe, pdbe.org); Protein Data Bank Japan (PDBj, pdbj.org); Electron Microscopy Data Bank (EMDB, emdb-empiar.org); and Biological Magnetic Resonance Bank (BMRB, bmrb.io)]. RCSB PDB serves as the wwPDB-designated Archive Keeper for the Protein Data Bank. Additional wwPDB Core Archives are as follows: Electron Microscopy Data Bank (wwPDB-designated Archive Keeper: EMDB) Biological Magnetic Resonance Bank (wwPDB-designated Archive Keeper: BMRB)

This dataset is about: Hydrochemistry and biological data measured on water bottle samples during METEOR cruise M10/2.

This dataset contains data of biological samples which were collected during scientific missions of JAMSTEC ships (NATSUSHIMA, KAIYO, YOKOSUKA, KAIREI and MIRAI) and submersibles.Data of this dataset is derived from the Marine Biological Sample Database of JAMSTEC. At the original database, you may search sample information such as number of individuals, preservation methods, sex, life stages, identification, collecting information and related literatures.

The header (line 1–9) contains general information about the study. Line 13–22 provide data items of different data types (column A). Column C presents item labels (en = english). Columns D,E,F contain semantic codes for each data item.

Supporting tables and figures. Table S1. The impact of different effect sizes on gene selection strategies when the sample size is fixed and relatively small. Mean (STD) of true positives computed from SIMU1 with 20 repetitions are reported. Sample size: . Total number of genes: 1000. Number of differentially expressed genes: 100. Number of permutations for Nstat: 10000. The significance threshold: 0.05. Table S2. The impact of different effect sizes on gene selection strategies when the sample size is fixed and relatively small. Mean (STD) of false positives computed from SIMU1 with 20 repetitions are reported. Sample size: . Total number of genes: 1000. Number of differentially expressed genes: 100. Number of permutations for Nstat: 10000. The significance threshold: 0.05. Table S3. The impact of different sample sizes on gene selection strategies when the effect size is fixed and relatively small. Mean (STD) of true positives computed from SIMU2 with 20 repetitions are reported. Effect size: . Total number of genes: 1000. Number of differentially expressed genes: 100. Number of permutations for Nstat: 10000. The significance threshold: 0.05. Table S4. The impact of different sample sizes on gene selection strategies when the effect size is fixed and relatively small. Mean (STD) of false positives computed from SIMU2 with 20 repetitions are reported. Effect size: . Total number of genes: 1000. Number of differentially expressed genes: 100. Number of permutations for Nstat: 10000. The significance threshold: 0.05. Table S5. The impact of different sample sizes on gene selection strategies when the effect size is fixed and relatively large. Mean (STD) of true positives computed from SIMU2 with 20 repetitions are reported. Effect size: . Total number of genes: 1000. Number of differentially expressed genes: 100. Number of permutations for Nstat: 10000. The significance threshold: 0.05. Table S6. The impact of different sample sizes on gene selection strategies when the effect size is fixed and relatively large. Mean (STD) of false positives computed from SIMU2 with 20 repetitions are reported. Effect size: . Total number of genes: 1000. Number of differentially expressed genes: 100. Number of permutations for Nstat: 10000. The significance threshold: 0.05. Table S7. The impact of different sample sizes on gene selection strategies with simulation based on biological data. Mean (STD) of true positives computed from SIMU-BIO with 20 repetitions are reported. Total number of genes: 9005. Number of permutations for Nstat: 100000. The significance threshold: 0.05. Table S8. The impact of different sample sizes on gene selection strategies with simulation based on biological data. Mean (STD) of false positives computed from SIMU-BIO with 20 repetitions are reported. Total number of genes: 9005. Number of permutations for Nstat: 100000. The significance threshold: 0.05. Table S9. The numbers of differentially expressed genes detected by different selection strategies. Total number of genes: 9005. Number of permutations for Nstat: 100000. The significance threshold: 0.05. Figure S1. Histogram of pairwise Pearson correlation coefficients between genes computed from HYPERDIP without normalization. Number of genes: 9005. Number of arrays: 88. (PDF)

Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.

Dataset contains dockside biological data for squid fishery from the years 1989 to 1994. This data and metadata were submitted by California Department of Fish and Wildlife (CDFW) Staff though the Data Management Plan (DMP) framework with the id: DMP000475. For more information, please visit https://wildlife.ca.gov/Data/Sci-Data.

This record is an overview entry for biological data collected on Southern Surveyor cruise SS 03/90. This cruise took place in the Gulf of Carpentaria, south eastern Arafura Sea and western Torres Strait during 19 November - 17 December 1990, under the leadership of Ian Poiner and Steve Blaber. Biological data collected on this cruise include hydrological data and samples from fish trawls, dredges and grabs. Please note: This metadata record is a preliminary entry derived from information in the cruise plan and/or cruise report. Individual data types - which may span several cruises - will be indexed separately within this metadata system in due course. - Biological Field Data Sheets recorded during this voyage have been scanned to PDF, and are available (to CSIRO Staff) on-line. See the details link under "Stored Media List" (below).

This record is an overview entry for biological data collected on Soela cruise SO 5/80. This cruise took place in the North West Shelf, the West Australian north coast and the Timor Sea during 21 June - 26 July 1980, under the leadership of W. Okera. Biological data collected on this cruise include EK 50 and Simrad 1100 acoustic data and observation data from the Atlas Fischfinder. Samples and biological data of 23 species of Carangidae, 4 species of Scombridae, at least 8 species of Leiognathidae, 6 species of clupeoids, 3 species of Sphyraenidae, 1 species of Trichiuridae, 1 species of Parastromateidae and 6-7 species of sharks. Plankton samples for abundance estimates. Bottom sediment samples from 60 dredge tows for particle size analysis, for determination of organic content and small sediment samples stained with Rose Bengol for foraminiferan studies. Photographs of 356 specimens representing about 290 species of both demersal and pelagic fish these were also retained for further examination.(derived from the cruise report). - Biological Field Data Sheets recorded during this voyage have been scanned to PDF, and are available (to CSIRO Staff) on-line. See the details link under "Stored Media List" (below).

This dataset contains ten years of physical, chemical, and biological data collected during shipboard surveys in Weeks Bay, Alabama, between June 1990 and May 2000. Surveys consisted of up to 19 stations throughout Weeks Bay and just beyond its mouth in Bon Secour Bay. Hydrographic profiles and water samples were collected at each station.

This record is an overview entry for biological data collected on Soela cruise SO 2/85. This cruise took place in waters off Tasmania, Bass Strait and the Tasman Sea (Cascade Plateau area) during 23 March - 21 April 1985, under the leadership of Ron Thresher and Steve Blaber. Biological data collected on this cruise include ichthyoplankton samples and fish samples from demersal and pelagic trawling. Electrophoretic samples of blue grenadier. EK 400 acoustic data of the Cascade Plateau area. Samples of fish including Orange Roughy, Ocean Perch, Spiky Dory, Blue Grenadier and Deep Sea Trevalla from the plateau area and a basalt sample for geological analysis.(derived from the cruise report) - Biological Field Data Sheets recorded during this voyage have been scanned to PDF, and are available (to CSIRO Staff) on-line. See the details link under "Stored Media List" (below).

This record is an overview entry for biological data collected on Southern Surveyor cruise SS 06/96. This cruise took place in waters off the east coast of Tasmania, south-eastern Victoria and southern New South Wales during 20 November - 19 December 1996, under the leadership of Alan Williams and Nic Bax. Biological data collected on this cruise include samples of fish and benthic invertebrates to determine the summer distribution and abundance of these fauna. Video and 35 mm camera photography, acoustic, biological and sediment samples to identify and determine the distribution of seafloor habitat types. Zooplankton samples to determine the summer distribution. Tissue samples from fish, plankton and seafoor invertebrates for stable isotopes analysis. Stomach samples from a diverse range of fish for dietary analysis. Phytoplankton samples for pigment analysis. Specimens for the "Field Guide to the Southeast Fishery" and "Handbook of Australian Seafood" projects including samples for fillet analysis, protein fingerprinting and genetic analysis. A collection of specimens for collaborative studies and for other institutions. Fish samples for ecomorphological analysis. Samples from 141 species of invertebrates for a bioprospecting project being undertaken by AIMS. Benthic samples and photographic images of the seafloor off Maria Island to study the abundance and pattern of distribution of brittle stars. Seal observations were also recorded during the cruise. Please note: This metadata record is a preliminary entry derived from information in the cruise plan and/or cruise report. Individual data types - which may span several cruises - will be indexed separately within this metadata system in due course.

This record is an overview entry for biological data collected on Southern Surveyor cruise SS 01/93. This cruise took place in waters off northern Queensland and the Gulf of Carpentaria during 11 January - 12 February 1993, under the leadership of John Salini. Biological data collected on this cruise include fish species composition and abundance data from 27 demersal trawls and benthic samples from dredging. RoxAnne acoustic data and hydrology samples. Seabird data from Magra and Saunders Islands. Data from the environmentally friendly net (EFN) and Engels net trawling trials including some video photography and benthic samples from dredging. Tissue samples from 143 Lutjanus malabaricus and 24 L. sebae and 63 other lutjanids (3 species) for population genetics studies. Numerous specimens were retained for the I. S. R. Munro Fish collection in Hobart and photographic images of the very large specimens. Cephalopods samples which consisted mainly of the loliginid squids. Please note: This metadata record is a preliminary entry derived from information in the cruise plan and/or cruise report. Individual data types - which may span several cruises - will be indexed separately within this metadata system in due course. - Biological Field Data Sheets recorded during this voyage have been scanned to PDF, and are available (to CSIRO Staff) on-line. See the details link under "Stored Media List" (below).

This record is an overview entry for biological data collected on Soela cruise SO 3/89. This cruise took place in waters off the east coast of Tasmania during 14 April - 8 May 1989, under the leadership of Nick Elliot, Clive Stanley and Brian Griffiths. Biological data collected on this cruise include 3229 kg of orange roughy from 15 stations around the St Patricks Head area. Orange roughy samples from Flinders Island area to determine if small roughy were present. The modal length of those caught was 20 cm, and only 5 were 15 cm or smaller. Biological samples, acoustic data and photography of a small aggregation of orange roughy near Bicheno. Plankton samples and hydrographic observations to study the relationship between krill and water masses off Tasman Island. Photography of bottom geological features. Acoustic data from the area of the orange roughy grounds. Please note: This metadata record is a preliminary entry derived from information in the cruise plan and/or cruise report. Individual data types - which may span several cruises - will be indexed separately within this metadata system in due course. - Biological Field Data Sheets recorded during this voyage have been scanned to PDF, and are available (to CSIRO Staff) on-line. See the details link under "Stored Media List" (below).

This record is an overview entry for biological data collected on Soela cruise SO 1/83. This cruise took place in the North West Shelf during 20 January - 2 March 1983, under the leadership of Tim Davis and Keith Sainsbury. Biological data collected on this cruise include composition and abundance data of demersal fish. Fish samples for biological studies (growth, reproduction and mortality). Zooplankton abundance data and larval fish samples. Carangid larvae for ageing studies. Lobster samples from six exploratory trawls. Lutjanus vitta and L. russelli for assessment of lunar periodicity of spawning. Prey availability and diet of Nemipterus peronii, N. tambuloides and Saurida undosquamis were examined in 6 areas. Fish specimens were obtained for stomach analysis, and benthic and epibenthic samples from the area. Dive observation data from an area adjacent to Bedout Island for experimental manipulation of epibenthos.(derived from the cruise report) - Biological data is available via Data Trawler. - Biological Field Data Sheets recorded during this voyage have been scanned to PDF, and are available on-line at http://www.marine.csiro.au/datacentre/process/data_files/BioData/log_sheet_scans/BOX_AB2009_550/BOX_AB2009_550_index.htm and http://www.marine.csiro.au/datacentre/process/data_files/BioData/log_sheet_scans/BOX_AB2009_551/BOX_AB2009_551_index.htm