cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.153827.v8
title: GenoCAD Tutorial

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.
DOI: 10.6084/m9.figshare.153059.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.119634
title: [Introduction to cancer molecular genetics. Genetic mechanisms of neoplasms] [Spanish]

description: Neoplasms are generally acquired genetically based processes that take place in multiple stages to achieve the capacity to metastasize. On most occasions, the morphological expression and genetic alterations underlying this evolutionary process are unknown, although certain "rules" general obtained in the study of tumors of certain sites (eg, colon) are applicable to most of neoplasms.<br>Cell neoplasms are diseases that affect basic processes that regulate replication and cell death (including the call immortality), cellular differentiation and motility, ability to induce neovascularization, as well as the maintenance of genomic integrity. All tumors have more than one abnormality in each of these basic aspects, in which more sequence alterations that is the sum of them in the same direction determines the appearance of the malignancy. Regulatory genes of these cellular functions are multiple and redundant, but can be classified into three main groups: oncogenes (tumor-inducing), tumor suppressor genes (tumor inhibitors) and genetic repair genes (responsible for maintaining the integrity of the genome).<br>The basic genetic mechanisms that have been described above responsible for alterations occur are equally varied and good activation of the tumor-inducing mechanisms lock mechanisms well inhibitors neoplasms or both aspects simultaneously. Defects in DNA repair contribute to a more rapid progression of the disease. Such mechanisms can be summarized as: changes in the genetic dose (gain / loss), gene fusion / rearrangements, injuries microsatellite mutations / nucleotide polymorphisms isolated, modifications of gene expression, epigenetic modifications, alterations and reactivation of mitochondrial genetic telomerase. In hereditary cancer syndromes, the initial genetic alteration appears in germline and normally it is a localized mutation in a tumor suppressor gene (except in the case of multiple endocrine neoplasia syndrome type 2 is an oncogene).
DOI: 10.6084/m9.figshare.153827.v9
title: GenoCAD Tutorial

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.
DOI: 10.6084/m9.figshare.121170.v1
title: [[Molecular pathology of endocrine tumors] [Spanish]

description: Endocrine neoplasms exhibit the same general type described abnormalities in most of malignant tumors. Many of these changes were initially described hereditary syndromes associated with tumors, and have been confirmed also in sporadic tumors.<br>Like most epithelial neoplasms, malignant transformation is the result of the accumulation of multiple genetic defects that determine the malignant cells do not respond and are independent of normal growth signals. Genetic alterations affecting oncogenes, tumor suppressor genes and gene repair. The molecular characterization of these defects has allowed to identify specific molecular mechanisms in these tissues and, in some cases, provide diagnostic and prognostic information very useful. The identification of germline mutations associated with multiple endocrine neoplasia syndromes types 1 and 2 has allowed the development of DNA tests to assess individuals at risk. In patients with medullary thyroid carcinoma, early thyroidectomy can be performed on the foundation provided by the analysis of DNA mutations (oncogene RET) when the tumor is still hidden and is curable.<br>The most frequent alterations have been associated with endocrine neoplasms are:<br>1. Genetic alterations associated with tumor initiation:<br>a. RET, RAS, fusion genes in thyroid neoplasms (RET / number in papillary carcinoma, PAX8/PPARg in follicular neoplasms).<br>b. Enzymes of the mitochondrial respiratory chain (SDHB/SDHD in paragangliomas, pheochromocytomas).<br>c. Enzymes for DNA replication and repair (Carney triad).<br>2. Genes associated with tumor progression: TP53, RB1.<br>3. Cell immortalization: reactivation of telomerase.
DOI: 10.6084/m9.figshare.107415
title: Efficient Cosmological Simulation Frameworks for Parameter Estimation

description: Poster for the 221st American Astronomical Society Meeting in January 2013. My goal for this poster is to outline methods to decrease by several orders of magnitude the numbers of large cosmological simulations needed to constrain cosmological and dark energy parameters from future surveys such as the Large Synoptic Survey Telescope, BigBOSS, and Euclid.
DOI: 10.6084/m9.figshare.107415.v1
title: Efficient Cosmological Simulation Frameworks for Parameter Estimation

description: Poster for the 221st American Astronomical Society Meeting in January 2013. My goal for this poster is to outline methods to decrease by several orders of magnitude the numbers of large cosmological simulations needed to constrain cosmological and dark energy parameters from future surveys such as the Large Synoptic Survey Telescope, BigBOSS, and Euclid.
DOI: 10.6084/m9.figshare.153827.v10
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.
DOI: 10.6084/m9.figshare.107066
title: Gaussian Job Archive for C12H12ClNO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.107065
title: Eisen 1995 RecA Evolution

description: Sequence alignments used in Eisen 1995. J Mol Evol. 1995 Dec;41(6):1105-23. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species.
DOI: 10.6084/m9.figshare.107066.v1
title: Gaussian Job Archive for C12H12ClNO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.107054
title: CNS Discovery Pipeline Supporting Data

description: These datasets describe the locations of conserved noncoding sequences identified in comparisons between orthologous genes in multiple plant species as well as comparisons between duplicated genes within a single species.
DOI: 10.6084/m9.figshare.107055
title: Code archive accompanying paper "High-Resolution Finite Volume Modeling of Wave Propagation in Orthotropic Poroelastic Media"

description: This is an archive of the code used to generate the results in the paper, "High-Resolution Finite Volume Modeling of Wave Propagation in Orthotropic Poroelastic Media," by Grady I. Lemoine, M. Yvonne Ou, and Randall J. LeVeque. All results presented in the paper can be obtained from the code stored here. This code requires version 4.6 of the CLAWPACK finite volume methods package to run.
DOI: 10.6084/m9.figshare.153827.v11
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.
DOI: 10.6084/m9.figshare.107034
title: 1000 Genomes Project Summary Statistics - 18th Jan 2013

description: There isn't a great deal of summary statistics data available on human-specific sequencing data. Here, I've tried to present something useful for me and hopefully others too. The .dat files are summaries produced from the 1000G project's ftp site (see link). Run the R script on the .dat files to produce the pdfs Many thanks to Sebastien Kurscheid for using his eutils-fu to produce summaries from the SRA (see other link).
DOI: 10.6084/m9.figshare.107034.v1
title: 1000 Genomes Project Summary Statistics - 18th Jan 2013

description: There isn't a great deal of summary statistics data available on human-specific sequencing data. Here, I've tried to present something useful for me and hopefully others too. The .dat files are summaries produced from the 1000G project's ftp site (see link). Run the R script on the .dat files to produce the pdfs Many thanks to Sebastien Kurscheid for using his eutils-fu to produce summaries from the SRA (see other link).
DOI: 10.6084/m9.figshare.107054.v1
title: CNS Discovery Pipeline Supporting Data

description: These datasets describe the locations of conserved noncoding sequences identified in comparisons between orthologous genes in multiple plant species as well as comparisons between duplicated genes within a single species.
DOI: 10.6084/m9.figshare.153827.v12
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.
DOI: 10.6084/m9.figshare.107035.v1
title: Interactions: The Cover Stories

description: Does being on the cover of Nature and Science ensure that a featured article gets online attention? This Interactions article looks at Altmetric data to find out whether cover features are guaranteed popularity. This article originally appeared as a blog post on the Altmetric blog.
DOI: 10.6084/m9.figshare.153827.v13
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.153827.v14
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.107016
title: The CGG KI Mouse Model does not show Learning and Memory Deficits on the Water maze or Motor Deficits on the Rotarod

description: In this study, CGG KI mice modeling the fragile X premutation were tested on the Morris water maze. There were no group differences among mutant mice and littermate controls during acquisition and the probe trial. Neither were there deficits for motor learning on the accelerating rotarod. Importantly, these same mice shows deficits for fine spatial processing using more sensitive behavioral assays (<em>Hunsaker MR, et al. Progressive spatial processing deficits in a mouse model of the fragile X premutation. Behav Neurosci. 2009 Dec;123(6):1315-24. doi: 10.1037/a0017616. PubMed PMID: 20001115; PubMed Central PMCID: PMC3410547</em>)
DOI: 10.6084/m9.figshare.107021
title: Growth of Short Read Archive since 2009 - Human Genomic and Exonic DNA - Total bases

description: Figure presenting the growth of total number of bases sequenced from human genomic and exonic DNA submitted to the NCBI Short Read Archive since 2009. The plots are based on SRA Run Summary numbers retrieved through the NCBI E-Utilities interface, sorted by year. Zip File contains the relevant data tables. Column "Total.Bases" was used for base counts in barplot. To reproduce in "R", unpack Zip file in working directory and execute attached R script. Related content (summary statistics of the 1000 Genomes Project) can be found at the link below - thanks to Chris Cole (Twitter @drchriscole).
DOI: 10.6084/m9.figshare.107011
title: Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

description: Supplemental data for Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts
DOI: 10.6084/m9.figshare.107016.v2
title: The CGG KI Mouse Model does not show Learning and Memory Deficits on the Water maze or Motor Deficits on the Rotarod

description: In this study, CGG KI mice modeling the fragile X premutation were tested on the Morris water maze. There were no group differences among mutant mice and littermate controls during acquisition and the probe trial. Neither were there deficits for motor learning on the accelerating rotarod. Importantly, these same mice shows deficits for fine spatial processing using more sensitive behavioral assays (<em>Hunsaker MR, et al. Progressive spatial processing deficits in a mouse model of the fragile X premutation. Behav Neurosci. 2009 Dec;123(6):1315-24. doi: 10.1037/a0017616. PubMed PMID: 20001115; PubMed Central PMCID: PMC3410547</em>)
DOI: 10.6084/m9.figshare.107021.v2
title: Growth of Short Read Archive since 2009 - Human Genomic and Exonic DNA - Total bases

description: Figure presenting the growth of total number of bases sequenced from human genomic and exonic DNA submitted to the NCBI Short Read Archive since 2009. The plots are based on SRA Run Summary numbers retrieved through the NCBI E-Utilities interface, sorted by year. Zip File contains the relevant data tables. Column "Total.Bases" was used for base counts in barplot. To reproduce in "R", unpack Zip file in working directory and execute attached R script. Related content (summary statistics of the 1000 Genomes Project) can be found at the link below - thanks to Chris Cole (Twitter @drchriscole).
DOI: 10.6084/m9.figshare.107011.v1
title: Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

description: Supplemental data for Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts
DOI: 10.6084/m9.figshare.107021.v1
title: Growth of Short Read Archive since 2009 - Human Genomic and Exonic DNA - Total bases

description: Figure presenting the growth of total number of bases sequenced from human genomic and exonic DNA submitted to the NCBI Short Read Archive since 2009. The plots are based on SRA Run Summary numbers retrieved through the NCBI E-Utilities interface, sorted by year,
DOI: 10.6084/m9.figshare.106988
title: Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe system

description: Supplemental data for Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe system
DOI: 10.6084/m9.figshare.107016.v1
title: The CGG KI Mouse Model does not show Learning and Memory Deficits on the Water maze or Motor Deficits on the Rotarod

description: In this study, CGG KI mice modeling the fragile X premutation were tested on the Morris water maze. There were no group differences among mutant mice and littermate controls during acquisition and the probe trial. Neither were there deficits for motor learning on the accelerating rotarod. Importantly, these same mice shows deficits for fine spatial processing using more sensitive behavioral assays (<em>Hunsaker MR, et al. Progressive spatial processing deficits in a mouse model of the fragile X premutation. Behav Neurosci. 2009 Dec;123(6):1315-24. doi: 10.1037/a0017616. PubMed PMID: 20001115; PubMed Central PMCID: PMC3410547</em>)
DOI: 10.6084/m9.figshare.107019.v1
title: TEST Kickoff report

description: Abstract: The ODIN kickoff meeting provided an overview of the current persistent identifier discussion, as well as valuable input from key stakeholders to the ODIN project. Eleven presenters from a variety of stakeholder groups provided important perspectives, and the extensive discussion by all meeting participants further elaborated on key points. Based on the key scientific inputs, the following actions were identified: i) Encourage discussion and collaboration between communities<br>ii) Address specific issues of working with large number of small heterogeneous datasets<br>iii) Identify main interoperability use cases and define their business value<br>iv) Encourage development of novel tools to track the reuse of data
DOI: 10.6084/m9.figshare.106978
title: Discovery of trypanosomatid parasites in globally distributed Drosophila species: Potential implications for research in neglected tropical diseases

description: Supplemental data for Discovery of trypanosomatid parasites in globally distributed Drosophila species: Potential implications for research in neglected tropical diseases
DOI: 10.6084/m9.figshare.106988.v1
title: Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe system

description: Supplemental data for Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe system
DOI: 10.6084/m9.figshare.106948
title: Supplementary Table S1

description: All proteins, possible glycosomal proteins, and a short list of glycosome membrane proteins.
DOI: 10.6084/m9.figshare.106949
title: Baess - A serial section analyser

description: A software package used to do simple, fast, analysis of serial sections.
DOI: 10.6084/m9.figshare.106978.v1
title: Discovery of trypanosomatid parasites in globally distributed Drosophila species: Potential implications for research in neglected tropical diseases

description: Supplemental data for Discovery of trypanosomatid parasites in globally distributed Drosophila species: Potential implications for research in neglected tropical diseases