cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/v1rjpf/whfik2
title: snk20160630_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pvnpwn
title: snk20160303_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kjfrfp
title: snk20150325_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ykodfc
title: snk20150602_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/26gvcw
title: snk20151107_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tmansw
title: snk20160216_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xyp9wj
title: snk20150205_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/plmhju
title: snk20151110_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hamwdr
title: snk20161118_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fyzv8j
title: snk20160129_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/eq2man
title: snk20150620_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jzwzok
title: snk20160610_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qhkeyh
title: snk20160704_03.txt.gz

description: :unav
DOI: 10.25386/genetics.11983857
title: Supplemental Material for Kontio, Rinta-aho, and Sillanpää, 2020

description: R-codes as simulated datasets used in the article and supplementary materials.
DOI: 10.7910/dvn/v1rjpf/yzmatd
title: snk20150411_03.txt.gz

description: :unav
DOI: 10.25386/genetics.11983857.v4
title: Supplemental Material for Kontio, Rinta-aho, and Sillanpää, 2020

description: R-codes as simulated datasets used in the article and supplementary materials.
DOI: 10.25386/genetics.11983857.v3
title: Supplemental Material for Kontio, Rinta-aho, and Sillanpää, 2020

description: R-codes as simulated datasets used in the article and supplementary materials.
DOI: 10.7910/dvn/v1rjpf/sdxhkc
title: snk20150131_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3968817
title: ecology 2050 lab 2

description: The Wind Speed is described using the Beaufort Scale (1 means light air and 4 refers to moderate breeze etc). For the insect abundance measurement using quadrats instead of cups to spot the number of insects during the trials.steps 1: using transects and spot the frequency of birds in grassland and woodlot.do 5 time in each area.2:using quadrats and record the frequency of insects in grassland and woodlot, choose 10 random location of each area.<br><br>
DOI: 10.7910/dvn/v1rjpf/g49hrb
title: snk20150304_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3968814
title: 88-gene matrix

description: Concatenated alignment of 88 genes for Wei et al. article, 'Plastid phylogenomics resolve deep relationships among eupolypod II ferns with rapid radiation and rate heterogeneity', submitted to <i>Genome Biology and Evolution</i>.<br>This version includes all introns in relevant genes.
DOI: 10.6084/m9.figshare.3968817.v1
title: ecology 2050 lab 2

description: The Wind Speed is described using the Beaufort Scale (1 means light air and 4 refers to moderate breeze etc). For the insect abundance measurement using quadrats instead of cups to spot the number of insects during the trials.steps 1: using transects and spot the frequency of birds in grassland and woodlot.do 5 time in each area.2:using quadrats and record the frequency of insects in grassland and woodlot, choose 10 random location of each area.<br><br>
DOI: 10.7910/dvn/v1rjpf/bcwnho
title: snk20161201_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3968808
title: Techniques & data: field sample training with animals (Quadrat and Distance Based)

description: The data was gathered roughly from 2:30pm to 4:40pm. The Wind Speed is described using the Beaufort Scale (1 means light air and 4 refers to moderate breeze). For the insect abundance measurement using quadrats only 1 species of insects were spotted during the trials. Next the 5 data points for the Distance-Based method were observed at 5 random spots in each of grassland and Woodlands. Also, random number generator was used to place the quadrat at 10 different locations within the grasslands and woodlands. Time refers to the amount of time that was spent observing each location for birds (in the Distance based technique ) and for insects in the Quadrat based technique.
DOI: 10.6084/m9.figshare.3968814.v2
title: 88-gene matrix

description: Concatenated alignment of 88 genes for Wei et al. article, 'Plastid phylogenomics resolve deep relationships among eupolypod II ferns with rapid radiation and rate heterogeneity', submitted to <i>Genome Biology and Evolution</i>.<br>This version includes all introns in relevant genes.
DOI: 10.6084/m9.figshare.3968808.v1
title: Techniques & data: field sample training with animals (Quadrat and Distance Based)

description: The data was gathered roughly from 2:30pm to 4:40pm. The Wind Speed is described using the Beaufort Scale (1 means light air and 4 refers to moderate breeze). For the insect abundance measurement using quadrats only 1 species of insects were spotted during the trials. Next the 5 data points for the Distance-Based method were observed at 5 random spots in each of grassland and Woodlands. Also, random number generator was used to place the quadrat at 10 different locations within the grasslands and woodlands. Time refers to the amount of time that was spent observing each location for birds (in the Distance based technique ) and for insects in the Quadrat based technique.
DOI: 10.6084/m9.figshare.3968814.v1
title: 88-gene matrix

description: Concatenated alignment of 88 genes for Wei et al. article, 'Chloroplast phylogenomics provides better resolutions for the deep phylogenetic relationships among eupolypod II ferns in the context of rapid radiation and rate variation', submitted to Cladistics.<br>This version includes all introns in relevant genes.
DOI: 10.7910/dvn/v1rjpf/4fiteb
title: snk20160209_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3968805
title: LESLIE OSEI DATASET 2 ECOLOGY INSECTS AND COLOURS.csv

description: <b>Variables</b> <b>Description</b> <b>Colour of bowl</b> There were 18 circular coloured bowls in total. The colours were Blue, Yellow and White. 9 bowls were placed in the grassland and were subdivided into 3 blue bowls, 3 yellow bowls and 3 white bowls. The other 9 bowls were placed in the woodlot and were subdivided into 3 blue bows, 3 yellow bowls and 3 white bowls. The bowls were sequentially placed together following the Blue, Yellow, White pattern. The pans were placed about one meter apart. <b>Type of Habitats</b> There were two distinct habitats and they served as an experimental ground. The habitats were grassland and woodlot. Grassland contained a lot of grasses and weeds with barely any trees. The ground was very dry. Woodlot was mostly made up of trees with barely any grasses and the soil was mostly moist. <b>Number of insects</b> The total number of insects in each colour bowl placed in the two distinct habitat and were counted and recorded in the data sheet. Most insects were found in either the yellow or white colour bowl <b>Number of rtus</b> RTU is the acronym for Recognizable Taxonomic Unit and this was calculated by analyzing the different species captured in each bowl. Hypothesis: There will be more insect captured if the pan traps used in this experiment was coloured as supposed to colourless. This is because insects are attracted to bright colours according to the Ultra Violet spectrum of light therefore, bright colours are the most reflected to their visual sensory organs. The experiment was conducted on September 28, 2016 at the York University Keele Campus Grassland and Woodlot between the hours of 3:00pm to 5:00 pm. The purpose of this experiment was to see the correlation between the number of insects captured and the colour of the circular bowl most animals are attracted to. The temperature was about 18 degrees Celsius and it was a windy day. The grassland was the first study site used. 9 circular coloured bowls were placed one meters apart from each other in a sequential order. The order was Blue, Yellow and White. The field consisted of 3 Blue bowls, 3 Yellow bowls and 3 white bowls. The second field study site was the woodlot. As described above, the sequential order and the same number of coloured bowls were placed on the woodlot. Each circular coloured bowl was filled with three quarters of soapy water. The study sites were revisited after an hour and half and each insect caught was recorded. The insects were viewed with the naked eye. The total number of insects caught on both grassland and woodlot were recorded in the data sheet for each colour bowl and its respective field of study. The number of different species caught on both field were also recorded for each colour bowl and its respective field of study. According to the data collected most of the animals were attracted to the yellow and white circular data bowl. There were more different species found in the White and yellow coloured bowl than the Blue bowl.
DOI: 10.7910/dvn/v1rjpf/wxq8ke
title: snk20160409_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/yubnn7
title: snk20150705_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rg9kes
title: snk20161213_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3954876
title: BIOL2050.lab3.Sweep nets.csv

description: <b>Meta-Data:</b><b><br></b><i>Trial:</i> indicates the number of trials that were conducted. A total of 20 trials were done. 10 of them were in Danby Grassland and 10 in Danby woodlot.<br><i>Site:</i> indicates the habitat that we collected our data from. Woodlot refers to Danby woodlot, and Grassland refers to Danby Grassland, both at York University Keele Campus.<i><br></i><i> Number of insects: </i>the total number of insects observed in the sweep net. <i><br></i><i>Number of insect species:</i> the number of different recognizable species was recorded for each trial. A total of four different species were observed, fly, Beetle, Caterpillar, and Mosquito.<br><br><b>Methods:</b> Two 25 meter transects were used in this experiment to serve as a path for the researchers to walk along. The two transects were 5 meters apart from each other. two members of our group walked along the transects holding sweep nets in their hands. They were swinging the nets back and forth to catch insects along the transects. the total number of insects was counted and recorded.<br>A total of 10 trials were conducted in Danby grassland, and a total of 10 other trials were conducted in Danby woodlot.<br>sweep nets were 30 cm in diameter and 70 cm in depth. The observed insects were categorized into four different species based on their morphological appearance. Thus, the collected data is categorical.<br>This field experiment started on September 28th, 2016at 2:30 PM and lasted for about an hours.<br>Weather condition: partly cloudy, windy, 20 degree Celsius.<br><b>Hypothesis:</b> Grassland habitat will have greater diversity of insects than woodlot habitat. This is because of the diversity of plant species and the absence of predators such as birds.<br><b>Predictions:</b>-The diversity of insects in grassland is larger than the diversity of insects in the woodlot.<br>- Grassland has a greater number of individuals.-The diversity of plant and vegetation in grassland support the abundance of insects.<br><br><br><br><br><br><br><br><br><br>
DOI: 10.7910/dvn/v1rjpf/c1wmhw
title: snk20150703_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3945030
title: Biol2050-Lab 3- Data Set 1.csv

description: <b>Method</b><b><br></b>The data collection was performed on September 28th, 2016 in the grassland and the woodlot area near York University. One meter by one meter metal quadrats were laid on the ground in random spots in the grassland and woodlot. This was done 10 times in the grassland and 10 times in the woodlot. The number of insects were counted as they were seen after 3 minutes maximum of looking in each quadrat then the number was counted and recorded. Then the number different recognizable taxonomic units within the insects observed in each quadrat were recorded.<br><b>Hypothesis</b><b><br></b>The number of recognizable taxonomic units in the woodlots is higher then that of the grassland. This is because of the cross of grassland dwelling insects into the woodlot giving the woodlot a higher diversity of insects with a similar number of insects.<b><br></b><b>Predictions</b><br>1. The insect species that live in the grassland can also be found in the woodlot<br>2. The amount of insects within a quadrat stays relatively the same across the grasslands and the woodlot.<b><br></b><b><br></b><br>
DOI: 10.6084/m9.figshare.3954876.v1
title: BIOL2050.lab3.Sweep nets.csv

description: <b>Meta-Data:</b><b><br></b><i>Trial:</i> indicates the number of trials that were conducted. A total of 20 trials were done. 10 of them were in Danby Grassland and 10 in Danby woodlot.<br><i>Site:</i> indicates the habitat that we collected our data from. Woodlot refers to Danby woodlot, and Grassland refers to Danby Grassland, both at York University Keele Campus.<i><br></i><i> Number of insects: </i>the total number of insects observed in the sweep net. <i><br></i><i>Number of insect species:</i> the number of different recognizable species was recorded for each trial. A total of four different species were observed, fly, Beetle, Caterpillar, and Mosquito.<br><br><b>Methods:</b> Two 25 meter transects were used in this experiment to serve as a path for the researchers to walk along. The two transects were 5 meters apart from each other. two members of our group walked along the transects holding sweep nets in their hands. They were swinging the nets back and forth to catch insects along the transects. the total number of insects was counted and recorded.<br>A total of 10 trials were conducted in Danby grassland, and a total of 10 other trials were conducted in Danby woodlot.<br>sweep nets were 30 cm in diameter and 70 cm in depth. The observed insects were categorized into four different species based on their morphological appearance. Thus, the collected data is categorical.<br>This field experiment started on September 28th, 2016at 2:30 PM and lasted for about an hours.<br>Weather condition: partly cloudy, windy, 20 degree Celsius.<br><b>Hypothesis:</b> Grassland habitat will have greater diversity of insects than woodlot habitat. This is because of the diversity of plant species and the absence of predators such as birds.<br><b>Predictions:</b>-The diversity of insects in grassland is larger than the diversity of insects in the woodlot.<br>- Grassland has a greater number of individuals.-The diversity of plant and vegetation in grassland support the abundance of insects.<br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.3945030.v1
title: Biol2050-Lab 3- Data Set 1.csv

description: <b>Method</b><b><br></b>The data collection was performed on September 28th, 2016 in the grassland and the woodlot area near York University. One meter by one meter metal quadrats were laid on the ground in random spots in the grassland and woodlot. This was done 10 times in the grassland and 10 times in the woodlot. The number of insects were counted as they were seen after 3 minutes maximum of looking in each quadrat then the number was counted and recorded. Then the number different recognizable taxonomic units within the insects observed in each quadrat were recorded.<br><b>Hypothesis</b><b><br></b>The number of recognizable taxonomic units in the woodlots is higher then that of the grassland. This is because of the cross of grassland dwelling insects into the woodlot giving the woodlot a higher diversity of insects with a similar number of insects.<b><br></b><b>Predictions</b><br>1. The insect species that live in the grassland can also be found in the woodlot<br>2. The amount of insects within a quadrat stays relatively the same across the grasslands and the woodlot.<b><br></b><b><br></b><br>
DOI: 10.7910/dvn/v1rjpf/kpkzgi
title: snk20150630_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3944262
title: Pan Trap Dataset

description: Ten bowls of different colors (yellow, white and blue) were placed in two different area types, grasslands, and woodlot. The bowls were filled half way with soapy water. The environmental conditions consisted of a moderate breeze and was slightly cloudy. After an hour of the bowls being placed, the amount of insects and the type of insects was recorded.<br>Variables:# of Species- The number of insects found in the bowls after an hour.Small Black flies- Insects in the bowls were smaller than average,and were a black shade with wings.Small brown flies- Insects in the bowls were smaller than average, and were a light brown shade with wings.Average size flies-Insects in bowls were average size flies, that had red eyes and wings.Other insects- The insects in the bowls were observed to be either beetles, ants, or unidentified insects.
DOI: 10.7910/dvn/v1rjpf/q9yz3u
title: snk20161110_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3944262.v1
title: Pan Trap Dataset

description: Ten bowls of different colors (yellow, white and blue) were placed in two different area types, grasslands, and woodlot. The bowls were filled half way with soapy water. The environmental conditions consisted of a moderate breeze and was slightly cloudy. After an hour of the bowls being placed, the amount of insects and the type of insects was recorded.<br>Variables:# of Species- The number of insects found in the bowls after an hour.Small Black flies- Insects in the bowls were smaller than average,and were a black shade with wings.Small brown flies- Insects in the bowls were smaller than average, and were a light brown shade with wings.Average size flies-Insects in bowls were average size flies, that had red eyes and wings.Other insects- The insects in the bowls were observed to be either beetles, ants, or unidentified insects.
DOI: 10.6084/m9.figshare.3939813
title: WHO IS THERE AND WHAT ARE THEY DOING? AN AGILE AND COMPUTATIONALLY EFFICIENT FRAMEWORK FOR GENOME DISCOVERY AND ANNOTATION FROM METAGENOMIC BIG DATA

description: Microbes are more abundant than any other biological guild, and in any environment it is important to understand which organisms are present, what they are doing, and how they are doing it. In many environments a majority of the microbial community members cannot be cultured. Metagenomics is a powerful tool to directly probe uncultured genomes and understand the diversity of microbial communities using only their DNA sequences. Analyzing the taxonomic and functional profiles present in a microbial community from unannotated shotgun sequencing reads is one of the goals in metagenomics, with extremely valuable applications in biological research such as medicine, biofuel, and ecology. Currently available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keeps increasing. This project aims to develop an agile and computationally efficient framework that integrates four methods that I have published (FOCUS, FOCUS2, Scaffold_builder, and SUPER-FOCUS) to recover, scaffold, and annotate genomes from metagenomes. In addition, the project aims to use the framework to create a database of new genomes from human microbiome and environmental samples.<br>
DOI: 10.7910/dvn/v1rjpf/g7ejvq
title: snk20150114_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3939813.v1
title: WHO IS THERE AND WHAT ARE THEY DOING? AN AGILE AND COMPUTATIONALLY EFFICIENT FRAMEWORK FOR GENOME DISCOVERY AND ANNOTATION FROM METAGENOMIC BIG DATA

description: Microbes are more abundant than any other biological guild, and in any environment it is important to understand which organisms are present, what they are doing, and how they are doing it. In many environments a majority of the microbial community members cannot be cultured. Metagenomics is a powerful tool to directly probe uncultured genomes and understand the diversity of microbial communities using only their DNA sequences. Analyzing the taxonomic and functional profiles present in a microbial community from unannotated shotgun sequencing reads is one of the goals in metagenomics, with extremely valuable applications in biological research such as medicine, biofuel, and ecology. Currently available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keeps increasing. This project aims to develop an agile and computationally efficient framework that integrates four methods that I have published (FOCUS, FOCUS2, Scaffold_builder, and SUPER-FOCUS) to recover, scaffold, and annotate genomes from metagenomes. In addition, the project aims to use the framework to create a database of new genomes from human microbiome and environmental samples.<br>
DOI: 10.7910/dvn/v1rjpf/viiepk
title: snk20161007_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/alycv8
title: snk20150811_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/scqzxz
title: snk20161106_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fol6lg
title: snk20160927_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/odtfub
title: snk20150207_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3920526
title: Maize Hybrid Imaging

description: Time course imaging of two maize inbreds and the F1 hybrid generated by crossing the two together.<br>For the purposes of generating this GIF, days with missing data were replaced with the image from the day previous to the gap. <br><br>
DOI: 10.7910/dvn/v1rjpf/upeeyx
title: snk20161005_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dunowu
title: snk20150715_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/uebi06
title: snk20160218_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pj8xdh
title: snk20160828_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/adt2sk
title: snk20150804_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3900036
title: Transcriptome - Pirum gemmata

description: - clean.fasta: Assembly cleaned from cross-contamination of other species multiplexed (Corallochytrium limacisporum Hawaii, Abeoforma whisleri and Parvularia atlantis [Nuclearia sp ATCC 50694]) after applying CroCo V0.1.1 (Simion et al. in prep).<br><br>- Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.<br>www.multicellgenome.com
DOI: 10.6084/m9.figshare.3899973
title: Rhizotron holder

description: Blueprint for a rhizotron holder to put in greenhouse. Cheap, easy to build and does not require much space.
DOI: 10.6084/m9.figshare.3900036.v1
title: Pirum gemmata's Transcriptome

description: - Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.
DOI: 10.7910/dvn/v1rjpf/qfsm9f
title: snk20160112_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3899973.v1
title: Rhizotron holder

description: Blueprint for a rhizotron holder to put in greenhouse. Cheap, easy to build and does not require much space.