960 research outputs found
raramayo/Bioinformatics: Bioinformatics_Fall_2021
No full textBioinformatics (BIOL651): Fall 2021
Instructor:
Name:
Dr. Rodolfo Aramayo, PhD
Email address:
[email protected]
Office hours:
By appointment
Office location:
Department of Biology
Room 412A, Biological Sciences Building West (BSBW)
Texas A&M University
College Station, TX 77843-3258
Related Courses:
BIOL650: Genomics
BIOL647: Digital Biology
To Do's:
Open an Account with: CYVERSE
Schedule:
DATE
LECTURE
TOPIC(s)
VIDEO(S)
Credits:
Training Materials - ENSEMBL
Introduction
Thu: 2021-10-07
Lecture01
Topic01: ENSEMBL - Introduction to Genome Browsers
Video
Topic02: ENSEMBL - Introduction to ENSEMBL
Video
Topic03: ENSEMBL - Classification of Genes and Transcripts
Video
Topic04: ENSEMBL - Introduction to Gene Annotation
Video
Topic05: ENSEMBL - Introduction to Comparative Genomics
Video
Topic06: ENSEMBL - Downloading Sequences
Video
Topic07: ENSEMBL - Special Note About Downloads
Video
Topic08: ENSEMBL - Comparative Genomics: Accessing Data
Video
Tue: 2021-10-12
Lecture02
Topic09: Introduction to CYVERSE
Topic10: CYVERSE - Genome Annotation
SEQUENCE
BRCA1 Region
Author: Rodolfo Aramayo ([email protected])
License: All content produced in this site is licensed by: CC BY-NC-SA 4.
A Re-Analysis of an Existing Drosophila melanogaster Dataset Reveals a New Set of Genes Involved in Post-Mating Response
No full textThe figures and tables presented here are part of a manuscript in preparation to be reported by Chloe J. Bennett and Rodolfo Aramayo entitled:
"A Re-Analysis of an Existing Drosophila melanogaster Dataset Reveals a New Set of Genes Involved in Post-Mating Response
AramayoLab/Compara_Lists: v1.0.0
No full text+TITLE: Compara_Lists
+AUTHOR: Rodolfo Aramayo
+EMAIL: [email protected]
Motivation
#+BEGIN_EXAMPLE
My main motivation for this script was reproducibility and replicability, when comparing list of
IDs. Mainly, I wanted to make sure that students evaluating different files used the same set of
commands, thus eliminating any possibility of error.
#+END_EXAMPLE
+BEGIN_SRC
ARAMAYO_LAB
This program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not,
see https://www.gnu.org/licenses/.
SCRIPT_NAME: Compara_Lists_v01.sh
SCRIPT_VERSION: 1.0
USAGE: ./Compara_Lists_v01.sh
-a List A # REQUIRED input (e.g., listA)
-A List A Name # OPTIONAL (e.g., listA)
-b List B # REQUIRED input (e.g., listB)
-B List B Name # OPTIONAL (e.g., listB)
TYPICAL COMMAND: Compara_Lists_v01.sh -a listA -A listA -b listB -B listB
INPUT01: -a FLAG REQUIRED input (e.g., listA)
INPUT01_DEFAULT: No Default. ListA file must be provided
INPUT01_FORMAT: Text file
INPUT01_NOTES: Single column text file
INPUT02: -A FLAG OPTIONAL (ListA_Label)
INPUT02_DEFAULT: listA
INPUT02_FORMAT: Text
INPUT02_NOTES: Optional
INPUT03: -b FLAG REQUIRED input (e.g., listB)
INPUT03_DEFAULT: No Default. ListB file must be provided
INPUT03_FORMAT: Text file
INPUT03_NOTES: Single column text file
INPUT04: -B FLAG OPTIONAL (ListB_Lable)
INPUT04_DEFAULT: listB
INPUT04_FORMAT: Text
INPUT04_NOTES: Optional
DEPENDENCIES: GNU COREUTILS Required (https://www.gnu.org/software/coreutils/)
Author: Rodolfo Aramayo
WORK_EMAIL: [email protected]
PERSONAL_EMAIL: [email protected]
+END_SRC
Development/Testing Environment
#+BEGIN_EXAMPLE
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
#+END_EXAMPLE
Script Dependencies
#+BEGIN_EXAMPLE
DEPENDENCIES: GNU COREUTILS Required (https://www.gnu.org/software/coreutils/)
#+END_EXAMPLE
GNU COREUTILS
* Version Numbers
#+BEGIN_EXAMPLE
comm (GNU coreutils) 8.30
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later https://gnu.org/licenses/gpl.html.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Richard M. Stallman and David MacKenzie.
+END_EXAMPLE
+BEGIN_EXAMPLE
comm (GNU coreutils) 8.32
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later https://gnu.org/licenses/gpl.html.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Richard M. Stallman and David MacKenzie.
+END_EXAMPL
Compara_lists
No full textScript Title: Compara_Lists
Organization: Aramayolab
Author: Rodolfo Aramayo
Work Email: [email protected]
Personal Email: [email protected]
License: Licensed under GPL-3.0-or-later
Objective:
The main objective for generating this script was reproducibility and replicability, when comparing
list of IDs. Mainly, I wanted to make sure that students evaluating information present in different
files used the same set of commands, thus eliminating any possibility of error
Documentation:
ARAMAYO_LAB
This program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not,
see .
SCRIPT_NAME: Compara_Lists_v01.sh
SCRIPT_VERSION: v1.0.1
USAGE: ${0}
-a List A # REQUIRED input (e.g., listA)
-A List A Name # OPTIONAL (e.g., listA)
-b List B # REQUIRED input (e.g., listB)
-B List B Name # OPTIONAL (e.g., listB)
TYPICAL COMMAND: Compara_Lists_v1.0.1.sh -a listA -A listA -b listB -B listB
INPUT01: -a FLAG Name of a single column text file containing records IDs to be compared (e.g., listA)
INPUT01_DEFAULT: No Default. ListA file must be provided
INPUT01_FORMAT: Single column text file
INPUT01_NOTES: Required
INPUT02: -A FLAG Name of the listA dataset or listA dataset label
INPUT02_DEFAULT: listA
INPUT02_FORMAT: Text
INPUT02_NOTES: Optional. Label will be used to name the output files
INPUT03: -b FLAG Name of a single column text file containing records IDs to be compared (e.g., listB)
INPUT03_DEFAULT: No Default. ListB file must be provided
INPUT03_FORMAT: Single column text file
INPUT03_NOTES: Required
INPUT04: -B FLAG Name of the listA dataset or listB dataset label
INPUT04_DEFAULT: listB
INPUT04_FORMAT: Text
INPUT04_NOTES: Optional. Label will be used to name the output files
DEPENDENCIES: GNU COREUTILS Required (https://www.gnu.org/software/coreutils/)
Author: Rodolfo Aramayo
WORK_EMAIL: [email protected]
PERSONAL_EMAIL: [email protected]
Development/Testing Environment:
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
Required Script Dependencies:
GNU COREUTILS (https://www.gnu.org/software/coreutils/)
Tested With Version Numbers: 8.30 and 8.32
8.30:
comm (GNU coreutils) 8.30
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later .
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Richard M. Stallman and David MacKenzie.
8.32:
comm (GNU coreutils) 8.32
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later .
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Richard M. Stallman and David MacKenzie
The Wine Attributes with the Greatest Influence in the Process of Consumer Choice in Spain
No full textThe commercialisation of wine in Spain is problematic due to two concrete circumstances: the decrease in wine consumption because of a consumer shift toward substitute drinks and the greater presence of national and foreign wine in the interior market, which involves an increase in business competitiveness. The increase in competitiveness of quality Spanish wine depends on producing enterprises’ knowledge of wine consumer preferences so they can offer consumers what they demand. In order to respond to this matter and better adapt supply, 421 wine consumers were surveyed using the Best-Worst Scaling methodology. Various segmentations were also made by consumer income and age groups. The results indicate that the two main attributes which condition consumers in choosing wine are the region of origin and having tasted it previously. The region of origin attribute is valued in general by consumers over 34 years old who have a monthly family income above 1,500 €. The attribute of having tasted it before, which on many occasions is associated with the price attribute, is valued particularly by younger consumers and those with lower incomes.Consumer behaviour, Wine attributes, Food Marketing, Consumer/Household Economics,
Fasta_Seq_Plot_Bash
No full text<h1><strong>Fasta_Seq_Plot_Bash</strong></h1>
<h2><strong>Motivation</strong></h2>
<pre><code>The primary objective behind creating this script was to facilitate the generation of 'pdf' or 'png' image files
depicting the size distribution of transcripts or proteins, excluding genomes, from fasta files.
</code></pre>
<h2>Documentation</h2>
<pre><code>########################################################################################################################################################################################################
ARAMAYO_LAB
This program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not,
see <https://www.gnu.org/licenses/>.
SCRIPT_NAME: Fasta_Seq_Plot_v1.0.0.sh
SCRIPT_VERSION: 1.0.0
USAGE: Fasta_Seq_Plot_v1.0.0.sh
-p Homo_sapiens.GRCh38.pep.all.fa # REQUIRED if -t Not Provided (Proteins File - Proteome)
-t Homo_sapiens.GRCh38.cds.all.fa # REQUIRED if -p Not Provided (Transcripts File - Transcriptome)
-n 'Homo sapiens' # REQUIRED (Species Name)
-z TMPDIR Location # OPTIONAL (default=0='Normal Run')
TYPICAL COMMANDS:
Fasta_Seq_Plot_v1.0.0.sh -p Homo_sapiens.GRCh38.pep.all.fa -n 'Homo sapiens'
Fasta_Seq_Plot_v1.0.0.sh -t Homo_sapiens.GRCh38.cds.all.fa -n 'Homo sapiens'
INPUT01: -p FLAG REQUIRED input ONLY if the '-t' flag associated file is not provided
INPUT01_FORMAT: Proteome Fasta File
INPUT01_DEFAULT: No default
INPUT02: -t FLAG REQUIRED input ONLY if the '-p' flag associated file is not provided
INPUT02_FORMAT: Transcriptome Fasta File
INPUT02_DEFAULT: No default
INPUT03: -n FLAG REQUIRED input
INPUT03_FORMAT: Text
INPUT03_DEFAULT: None
INPUT03_NOTES: The text should correspond to the species name whose fasta file is being analyzed
INPUT03_NOTES: If the text provided is composed on more than one word (e.g., Genus species), then the text must be within single or double quotes
INPUT04: -z FLAG OPTIONAL input
INPUT04_FORMAT: Numeric: 0 == Normal Run | 1 == TMPDIR Run
INPUT04_DEFAULT: 0 == Normal Run
INPUT04_NOTES: 0 Processes the data in the same directory where the script is being run
INPUT04_NOTES: 1 Processes the data in the /var/folders/ct/4v6y_c6s2tl1ns6t2yz3qmd80000gn/T/ directory of the computer used or of the node assigned by the SuperComputer scheduler
INPUT04_NOTES: Processing the data in the /var/folders/ct/4v6y_c6s2tl1ns6t2yz3qmd80000gn/T/ directory of the node assigned by the SuperComputer scheduler reduces the possibility of file error generation due to network traffic
DEPENDENCIES: GNU AWK: Required (https://www.gnu.org/software/gawk/)
GNU COREUTILS: Required (https://www.gnu.org/software/coreutils/)
datamash: Required (http://www.gnu.org/software/datamash)
R: Required (https://www.r-project.org/)
Assumes that the packages tidyverse, ggplot2, and ggeasy are already installed
Author: Rodolfo Aramayo
WORK_EMAIL: [email protected]
PERSONAL_EMAIL: [email protected]
########################################################################################################################################################################################################
</code></pre>
<h2>Development/Testing Environment:</h2>
<pre><code>Distributor ID: Apple, Inc.
Description: Apple M1 Max
Release: 14.4.1
Codename: Sonoma
</code></pre>
<pre><code>Distributor ID: Ubuntu
Description: Ubuntu 22.04.3 LTS
Release: 22.04
Codename: jammy
</code></pre>
<h2>Required Script Dependencies:</h2>
<h3>GNU COREUTILS (https://www.gnu.org/software/coreutils/)</h3>
<h4>Version Number: 8.30</h4>
<pre><code>(GNU coreutils) 9.4
Copyright (C) 2023 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Richard M. Stallman and David MacKenzie.
</code></pre>
<h3>GNU AWK (https://www.gnu.org/software/gawk/)</h3>
<h4>Version Number: 5.3.0, API 4.0</h4>
<pre><code>GNU Awk 5.3.0, API 4.0
Copyright (C) 1989, 1991-2023 Free Software Foundation.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/.
</code></pre>
<h3>DATAMASH ( (http://www.gnu.org/software/datamash)</h3>
<h4>Version Number: datamash (GNU datamash) 1.8-dirty</h4>
<pre><code>datamash (GNU datamash) 1.8-dirty
Copyright (C) 2022 Assaf Gordon and Tim Rice
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Assaf Gordon, Tim Rice, Shawn Wagner, Erik Auerswald.
</code></pre>
<h3>R (https://www.r-project.org/)</h3>
<h4>Version Number: R version 4.3.3 (2024-02-29) -- "Angel Food Cake"</h4>
<pre><code>R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
</code></pre>
<h3>R - ggplot2 (https://github.com/tidyverse/ggplot2)</h3>
<h4>Version Number: 3.5.0</h4>
<pre><code>Package: ggplot2
Version: 3.5.0
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
</code></pre>
<h3>R - ggeasy (https://github.com/jonocarroll/ggeasy)</h3>
<h4>Version Number: 0.1.4</h4>
<pre><code>Package: ggeasy
Title: Easy Access to 'ggplot2' Commands
Version: 0.1.4
</code></pre>If you use this software, please cite it as below
Dr. Rodolfo D. Torres talk at University of Washington Tacoma: After Latino Metropolis
No full textThe role of class and spatial politics in Latino Los Angeles will be the subject of this timely talk. Professor Rodolfo D. Torres is co-author of the highly acclaimed book, Latino Metropolis (University of Minnesota Press, 2000). He will revisit this important book
How corporate governance and globalization can run afoul of the law and good practices in business: The Enron's disgraceful affair.
No full textThe purpose of this paper is to set out the Enron’s demise into the perspective of Corporate and Global Governance. To accomplish this target, the incremental cash flow model is expanded to give room for governance issues, while a functional introduction to information sets is developed, including bounded rationality, asymmetric information, opportunistic behavior, transaction costs and agency problems. Then, corporate governance is linked to globalization by means of some recent approaches that go beyond a narrow economic mindset to encompass a far-reaching dynamics. Taking advantage of such background, the Enron’s story is tracked down over a span of fifteen years since its starting day to its bankruptcy filing. Leading events are explained from corporate and global governance viewpoints, while an in-depth analysis is worked out on Enron’s complex game of deception and breach of contracts: the outrageous affiliated limited partnerships, the lavish pay package to its executives, the involvement with global governance through the Indian affair and the Taliban connection. It is for the incremental cash flow model to explain malfeasance with cash flows from assets, and how cash flows to creditors were actually contrived. Furthermore, to highlight how cash flows were swindled from stockholders and, finally, how Enron made wheeling and dealing with cash flows on behalf of its managers.corporate governance, global governance, incremental cash flow model, globalization, information sets, good practices.
Ideales platónicos y ensoñaciones rousseaunianas en el pensamiento político de Kant
No full textEn este trabajo se rastrean las improntas dejadas en el pensamiento político kantiano por ciertas consideraciones de Platón y de Rousseau, que aquí hemos dado en identificar como ideales y ensoñaciones, con la convicción de que los ideales republicanos del primero influyeron en el segundo y habrían llegado por ese conductor a la reflexión práctica de Kant. La revolución interior que, según Kant, cada uno de nosotros verifica alrededor de los cuarenta años, habría tenido como un factor determinante en su propio caso la lectura de Rousseau, que Kant realiza justamente cuando muere uno de sus amigos más cercanos y queda impactado por esa pérdida. En este contexto cobra cuerpo una relativamente desatendida preocupación kantiana por la desigualdad y la injusticia social, que han estudiado por ejemplo entre nosotros María Julia Bertomeu y Nuria Sánchez Madrid.Este trabajo se adscribe a los Proyectos de Investigación Philosophy of History and Globalisation of Knowledge. Cultural Bridges Between Europe and Latin America: WORLDBRIDGES (F7-PEOPLE-2013-IRSES: PIRSES-GA-2013-612644) y Prismas filosófico-morales de las crisis: Hacia una nueva pedagogía sociopolítica (FFI2013-42395-P). También se inscribe en el proyecto sobre Kant, sus clásicos y el clasicismo promovido por CTK E-Books (www.contextoskantianos.net), y que tuvo lugar en la Universidad de Los Andes (Bogotá, Colombia) a finales de mayo de 2015, organizado por Rodolfo Arango y Catalina González, con la participación de Roberto R. Aramayo, Luis Eduardo Molina, Efraín Lazos, Lisímaco Parra, Pablo Oyarzun y Luis Placencia.
Roberto Rodríguez Aramayo, Research Profesor at the IFS-CCHS/CSIC. http://ifs.csic.es/es/personal/robertor.aramayo / - http://orcid.org/0000-0002-4771-830
Rodolfo Lenz
No full textIn this article the author intends to offer an overall profile of Dr. Rodolfo
Lenz’ versatile personality, portraying him as the man, the phonetician, the
expert scholar in Araucanian, the orthographer, the methodologist, the
compulsive scientist. All these personality traits contributed to renovate in
Chile the interest in language, in foreign language methodology and the
institutionalization of folklore as a science, which earned him the Chilean
nationalityEn este trabajo el autor se propone dar una visión de conjunto de la polifacética
personalidad del Dr. Rodolfo Lenz: el hombre, el fonetista, el araucanista, el
lexicógrafo, el gramático, el ortógrafo, el metodólogo, el científico compulsivo.
Aspectos todos que contribuyeron a renovar profundamente en Chile el
estudio de las ciencias del lenguaje, la metodología de la enseñanza de las
lenguas extranjeras y la fundación del folclor como ciencia, por todo lo cual
el Gobierno le confirió nuestra nacionalida
- …
