cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.153834
title: Copy of BS-Seq & MethylC-Seq public datasets

description: I started this spreadsheet over a year ago, towards the beginning of my PhD. It has details and links to some (most?) of the publicly available whole-genome bisulfite-sequencing data sets in human. I haven’t updated it in a while but I figured it might be of use to others in its current form. I initially blogged about this here http://peterhickey.me/2012/12/12/publicly-available-whole-genome-bisulfite-sequencing-data/ See the link for the Google Doc version of this file.
DOI: 10.6084/m9.figshare.153907.v3
title: insol_0.91

description: R package to compute Incoming Solar Radiation (insolation) for paleoclimate studies. Features three solutions: BER78, BER90 and LA04. Computes daily-mean, season-averaged and annual means for all latitudes. Licenced under MIT licence. Refer to original papers when using specific insolation solutions.
DOI: 10.6084/m9.figshare.153828.v1
title: Spatial Networks

description: Network datasets and meta data using in work which develops a new model of spatial network structure: http://arxiv.org/abs/1210.4246
DOI: 10.6084/m9.figshare.153834.v1
title: Copy of BS-Seq & MethylC-Seq public datasets

description: I started this spreadsheet over a year ago, towards the beginning of my PhD. It has details and links to some (most?) of the publicly available whole-genome bisulfite-sequencing data sets in human. I haven’t updated it in a while but I figured it might be of use to others in its current form. I initially blogged about this here http://peterhickey.me/2012/12/12/publicly-available-whole-genome-bisulfite-sequencing-data/ See the link for the Google Doc version of this file.
DOI: 10.6084/m9.figshare.153827
title: GenoCAD Tutorials

description: This tutorial includes two PowerPoint presentations developed by Mary Mangan from OpenHelix. Students should start with the Introduction prior to moving on to the Advanced tutorial. The slides decks include numerous comments that will help students go through the tutorials. In order to perform the hands on activities students need to download the GenoCAD Training Set. This dataset includes a list of parts and a grammar used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.genocad) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace. The tutorial also includes a series of additional exercises that will be used to reinforce the concepts introduced in the tutorial. Please visit the GenoCAD page for videos of the tutotials.
DOI: 10.6084/m9.figshare.153907.v4
title: Paleoclimate insolation calculation

description: R package to compute Incoming Solar Radiation (insolation) for paleoclimate studies. Features three solutions: BER78, BER90 and LA04. Computes daily-mean, season-averaged and annual means for all latitudes. Licenced under MIT licence. Refer to original papers when using specific insolation solutions.
DOI: 10.6084/m9.figshare.153835.v1
title: Rhesus Gastric Microbiome

description: This data is part of the projet to study the rhesus gastric microbiome and the effects of <em>Helicobacter pylori</em> on it.
DOI: 10.6084/m9.figshare.153822.v1
title: Parametrisierung orographischen Schwerewellen

description: diploma thesis
DOI: 10.6084/m9.figshare.153827.v1
title: GenoCAD Training Set I

description: This fileset includes a grammar file (.zip) and a list of parts used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.zip) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". 7- Click on "1-Parts" to return to the parts management tool. 8- On the Libraries tab, click on the "New Library" button. 9- Select the "Training Set E.Coli v3" grammar and give a name to the parts library such as "Training Set Parts Library". 10- Click on the "My Parts" tab and click on the "Import parts" button. 11- Select the "Training Set Parts Library" parts library and the tab-delimited option. Select the Training_Set_Parts_v3.txt file and click import. Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace.
DOI: 10.6084/m9.figshare.153835.v3
title: Rhesus Gastric Microbiome

description: This data is part of the projet to study the rhesus gastric microbiome and the effects of <em>Helicobacter pylori</em> on it.
DOI: 10.6084/m9.figshare.153822.v2
title: Parametrisierung orographischer Schwerewellen

description: diploma thesis
DOI: 10.6084/m9.figshare.153821.v1
title: git can facilitate greater reproducibility and increased transparency in science

description: Pre-print of my article describing how git can be used to improve science.
DOI: 10.6084/m9.figshare.153827.v2
title: GenoCAD Training Set I

description: This fileset includes a grammar file (.zip) and a list of parts used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.zip) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". 7- Click on "1-Parts" to return to the parts management tool. 8- On the Libraries tab, click on the "New Library" button. 9- Select the "Training Set E.Coli v3" grammar and give a name to the parts library such as "Training Set Parts Library". 10- Click on the "My Parts" tab and click on the "Import parts" button. 11- Select the "Training Set Parts Library" parts library and the tab-delimited option. Select the Training_Set_Parts_v3.txt file and click import. Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace.
DOI: 10.6084/m9.figshare.153835.v2
title: Rhesus Gastric Microbiome

description: This data is part of the projet to study the rhesus gastric microbiome and the effects of <em>Helicobacter pylori</em> on it.
DOI: 10.6084/m9.figshare.153821.v2
title: git can facilitate greater reproducibility and increased transparency in science

description: Pre-print of my article describing how git can be used to improve science.
DOI: 10.6084/m9.figshare.153822.v3
title: Parametrisierung orographischer Schwerewellen

description: diploma thesis
DOI: 10.6084/m9.figshare.153799
title: Gaussian Job Archive for C2H6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153827.v3
title: GenoCAD Training Set I

description: This dataset includes a list of parts and a grammar used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.zip) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace.
DOI: 10.6084/m9.figshare.153821.v3
title: git can facilitate greater reproducibility and increased transparency in science

description: Pre-print of my article describing how git can be used to improve science. Manuscript is currently in review at Source Code in Medicine and Biology.
DOI: 10.6084/m9.figshare.153796
title: Post-training sucrose-conditioned cues experiment

description: This experiment tested the hypothesis that exposure to sucrose conditioned cues would modulate memory in the same way as consumption of sucrose did in Experiment 1.
DOI: 10.6084/m9.figshare.153798
title: Gaussian Job Archive for C2H6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153799.v1
title: Gaussian Job Archive for C2H6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153796.v1
title: Post-training sucrose-conditioned cues experiment

description: This experiment tested the hypothesis that exposure to sucrose conditioned cues would modulate memory in the same way as consumption of sucrose did in Experiment 1.
DOI: 10.6084/m9.figshare.153798.v1
title: Gaussian Job Archive for C2H6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153827.v4
title: GenoCAD Training Set I

description: This dataset includes a list of parts and a grammar used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.zip) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace.
DOI: 10.6084/m9.figshare.153792
title: Conflicting data of population trends in amphibian species in the Global Amphibian Assessment

description: 18 August 2005 Data derived from the Global Amphibian Assessment. (Stuart, S. N., J. S. Chanson, N. A. Cox, B. E. Young, A. S. L. Rodriguez, D. L. Fischman, and R. W. Waller. 2004. Status and trends of amphibian declines and extinctions worldwide. Science 306:1783-1786. DOI: 10.1126/science.1103538) Columns: Species<br>Order<br>Family<br>Red List Category<br>Red List Criteria<br>Rationale<br>Population Trend - Reported population trend<br>Population Trend Info - Additional information related to the 'Population Trend' field<br>Population Trend Evidence - Evidence given to justify the population trend given<br>Population Trend Conflict - Rows with a value of '1' have a conflict between the 'Population Trend' and the data given (for example: Acanthixalus spinosus was listed as 'Decreasing', but further information said 'This is a hard species to find, and so its abundance is unclear.') Note: Taxonomic names and classifications are as they were mid-2005. Please consult resources like the Amphibian Species of the World (research.amnh.org/vz/herpetology/amphibia/) for the current classification and history. For further information and context, see letter with DOI: 10.6084/m9.figshare.153793
DOI: 10.6084/m9.figshare.153795
title: Post-training sucrose experiment

description: This experiment compared the effects of immediate and delayed post-training consumption of sucrose on memory for a conditioned cue preference (CCP).
DOI: 10.6084/m9.figshare.153791
title: Conflicting data of chytridiomycosis infection and risk in amphibian species in the Global Amphibian Assessment

description: 18 August 2005 Data derived from the Global Amphibian Assessment. (Stuart, S. N., J. S. Chanson, N. A. Cox, B. E. Young, A. S. L. Rodriguez, D. L. Fischman, and R. W. Waller. 2004. Status and trends of amphibian declines and extinctions worldwide. Science 306:1783-1786. DOI: 10.1126/science.1103538) Columns: Species<br>Notes<br>Evidence_ID - Index of column 'Evidence'<br>Evidence - Evidence given to justify listing the species as under risk of chytridiomycosis Note: Taxonomic names and classifications are as they were mid-2005. Please consult resources like the Amphibian Species of the World (research.amnh.org/vz/herpetology/amphibia/) for the current classification and history. For further information and context, see letter with DOI: 10.6084/m9.figshare.153793
DOI: 10.6084/m9.figshare.153795.v1
title: Post-training sucrose experiment

description: This experiment compared the effects of immediate and delayed post-training consumption of sucrose on memory for a conditioned cue preference (CCP).
DOI: 10.6084/m9.figshare.153827.v5
title: GenoCAD Tutorial I

description: This dataset includes a list of parts and a grammar used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.zip) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace.
DOI: 10.6084/m9.figshare.153788
title: Puerto Rican Eleutherodactulus frogs abundance

description: This dataset is the relative abundance of two frog species (Eleutherodactulus coqui and E. cochranae) collected using visual encounter surveys between the years 1996 and 2000. The site was a ground bromeliad garden of approximately 36 m^2 in front of the Chancelor's House of the Rio Piedras campus of the University of Puerto Rico. Approximate coordinates, obtained with Google Maps, are: 18.4039, -66.0490 The data was collected as a long-term undergrad project. Columns:<br>DATE_YYYYMMDD - Date in format YearMonthDay<br>NOAA_PRECIP - Precipitation (inches) from the Río Piedras weather station (see notes below)<br>NOAA_TEMPMIN - Minimum temperature (degrees F) from the Río Piedras weather station (see notes below)<br>NOAA_TEMPMAX - Maximum temperature (degrees F) from the Río Piedras weather station (see notes below)<br>TEMP - Temperature (degrees C) measured with an electronic handheld meter (model not recorded) at the site at the moment of the survey<br>RH - Relative humidity (%) measured with an electronic handheld meter (model not recorded) at the site at the moment of the survey<br>CH_TOTAL - Total number of 'Eleutherodactylus cochranae' individuals seen<br>CH_CALLINGMALES - Number of 'Eleutherodactylus cochranae' calling males seen<br>CH_MALES - Number of 'Eleutherodactylus cochranae' males seen<br>CH_FEMALES - Number of 'Eleutherodactylus cochranae' female seen<br>CH_GRAVIDFEMALES - Number of 'Eleutherodactylus cochranae' gravid females seen<br>CH_JUVENILES - Number of 'Eleutherodactylus cochranae' juveniles seen<br>CQ_TOTAL - Total number of 'Eleutherodactylus coqui' individuals seen<br>CQ_MALES - Number of 'Eleutherodactylus coqui' males seen<br>CQ_CALLINGMALES - Number of 'Eleutherodactylus coqui' calling males seen<br>CQ_FEMALES - Number of 'Eleutherodactylus coqui' females seen<br>CQ_GRAVIDFEMALES - Number of 'Eleutherodactylus coqui' gravid females seen<br>CQ_JUVENILES - Number of 'Eleutherodactylus coqui' juveniles seen<br>GRAND_TOTAL - Total number of 'Eleutherodactylus coqui' and 'Eleutherodactylus cochranae' individuals seen Weather Station: We used the "Rio Piedras Experimental Station" weather station, listed as "RIO PIEDRAS EXP STA". Since the survey was at night, we used the data from the next day as a better aproximation of the conditions during the survey and to get the precipitation that may have fallen during that night. The data was extracted from the Climatological Data publication from NOAA. Several undergraduate and graduate students of the Department of Biology of the UPRRP helped to collect this data: V. Rentas-Sanabria, L. Jaramillo, J. Billoch, F. C. Li-Objio, M. Cardona-Maldonado, M. Ramos, A. León-Cardona, J. Delgado-Acevedo, and N. Ríos-López. This research was funded by the Ronald E. McNair Post-Baccaulaurate Achievement Program, Puerto Rico Louis Stokes Alliance for Minority Participation Program, Proyecto Coquí, and the Dean of Graduate Studies and Research, all at the University of Puerto Rico, Río Piedras.
DOI: 10.6084/m9.figshare.153791.v1
title: Conflicting data of chytridiomycosis infection and risk in amphibian species in the Global Amphibian Assessment

description: 18 August 2005 Data derived from the Global Amphibian Assessment. (Stuart, S. N., J. S. Chanson, N. A. Cox, B. E. Young, A. S. L. Rodriguez, D. L. Fischman, and R. W. Waller. 2004. Status and trends of amphibian declines and extinctions worldwide. Science 306:1783-1786. DOI: 10.1126/science.1103538) Columns: Species<br>Notes<br>Evidence_ID - Index of column 'Evidence'<br>Evidence - Evidence given to justify listing the species as under risk of chytridiomycosis Note: Taxonomic names and classifications are as they were mid-2005. Please consult resources like the Amphibian Species of the World (research.amnh.org/vz/herpetology/amphibia/) for the current classification and history. For further information and context, see letter with DOI: 10.6084/m9.figshare.153793
DOI: 10.6084/m9.figshare.153827.v6
title: GenoCAD Tutorial I

description: This tutorial includes a PowerPoint presentation developed by Mary Mangan from OpenHelix. The slides deck includes numerous comments that will help students go through the tutorial. In order to perform the hands on activities students need to download the GenoCAD Training Set. This dataset includes a list of parts and a grammar used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.zip) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace. The tutorial also includes a series of additional exercises that will be used to reinforce the concepts introduced in the tutorial.
DOI: 10.6084/m9.figshare.153788.v1
title: Puerto Rican Eleutherodactulus frogs abundance

description: This dataset is the relative abundance of two frog species (Eleutherodactulus coqui and E. cochranae) collected using visual encounter surveys between the years 1996 and 2000. The site was a ground bromeliad garden of approximately 36 m^2 in front of the Chancelor's House of the Rio Piedras campus of the University of Puerto Rico. Approximate coordinates, obtained with Google Maps, are: 18.4039, -66.0490 The data was collected as a long-term undergrad project. Columns:<br>DATE_YYYYMMDD - Date in format YearMonthDay<br>NOAA_PRECIP - Precipitation (inches) from the Río Piedras weather station (see notes below)<br>NOAA_TEMPMIN - Minimum temperature (degrees F) from the Río Piedras weather station (see notes below)<br>NOAA_TEMPMAX - Maximum temperature (degrees F) from the Río Piedras weather station (see notes below)<br>TEMP - Temperature (degrees C) measured with an electronic handheld meter (model not recorded) at the site at the moment of the survey<br>RH - Relative humidity (%) measured with an electronic handheld meter (model not recorded) at the site at the moment of the survey<br>CH_TOTAL - Total number of 'Eleutherodactylus cochranae' individuals seen<br>CH_CALLINGMALES - Number of 'Eleutherodactylus cochranae' calling males seen<br>CH_MALES - Number of 'Eleutherodactylus cochranae' males seen<br>CH_FEMALES - Number of 'Eleutherodactylus cochranae' female seen<br>CH_GRAVIDFEMALES - Number of 'Eleutherodactylus cochranae' gravid females seen<br>CH_JUVENILES - Number of 'Eleutherodactylus cochranae' juveniles seen<br>CQ_TOTAL - Total number of 'Eleutherodactylus coqui' individuals seen<br>CQ_MALES - Number of 'Eleutherodactylus coqui' males seen<br>CQ_CALLINGMALES - Number of 'Eleutherodactylus coqui' calling males seen<br>CQ_FEMALES - Number of 'Eleutherodactylus coqui' females seen<br>CQ_GRAVIDFEMALES - Number of 'Eleutherodactylus coqui' gravid females seen<br>CQ_JUVENILES - Number of 'Eleutherodactylus coqui' juveniles seen<br>GRAND_TOTAL - Total number of 'Eleutherodactylus coqui' and 'Eleutherodactylus cochranae' individuals seen Weather Station: We used the "Rio Piedras Experimental Station" weather station, listed as "RIO PIEDRAS EXP STA". Since the survey was at night, we used the data from the next day as a better aproximation of the conditions during the survey and to get the precipitation that may have fallen during that night. The data was extracted from the Climatological Data publication from NOAA. Several undergraduate and graduate students of the Department of Biology of the UPRRP helped to collect this data: V. Rentas-Sanabria, L. Jaramillo, J. Billoch, F. C. Li-Objio, M. Cardona-Maldonado, M. Ramos, A. León-Cardona, J. Delgado-Acevedo, and N. Ríos-López. This research was funded by the Ronald E. McNair Post-Baccaulaurate Achievement Program, Puerto Rico Louis Stokes Alliance for Minority Participation Program, Proyecto Coquí, and the Dean of Graduate Studies and Research, all at the University of Puerto Rico, Río Piedras.
DOI: 10.6084/m9.figshare.153786
title: Gaussian Job Archive for C12H14Cl2N2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153827.v7
title: GenoCAD Tutorial I

description: This tutorial includes a PowerPoint presentation developed by Mary Mangan from OpenHelix. The slides deck includes numerous comments that will help students go through the tutorial. In order to perform the hands on activities students need to download the GenoCAD Training Set. This dataset includes a list of parts and a grammar used as part of the GenoCAD Introductory tutorial. In order to import this data set in GenoCAD, proceed as follows: 1- Log into GenoCAD, create an account if you don't already have one. 2- Click on the Parts tab. 3- Click on the Grammars tab. 4- Click on the Add/Import Grammar button. 5- Using the "choose file" button, select the grammar file (.genocad) and click on import grammar. 6- Click on "use existing icon set" and click on "continue import". Upon completion of this procedure you should have a new grammar with a library of 37 parts in your workspace. The tutorial also includes a series of additional exercises that will be used to reinforce the concepts introduced in the tutorial.
DOI: 10.6084/m9.figshare.153101
title: Gaussian Job Archive for C8H13Cl

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153786.v1
title: Gaussian Job Archive for C12H14Cl2N2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153059
title: Gaussian Job Archive for C8H13Cl

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153101.v1
title: Gaussian Job Archive for C8H13Cl

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153785
title: Gaussian Job Archive for C12H12ClNO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.