98 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
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
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
Politics climates and philosophical responsibilities: the Cassirer's lecture on Philosophy and Politics (1944)
No full textEste artículo está sujeto a una licencia CC BY 4.0[EN] In his speech of 1944 on Philosophy and Politics, Ernst Cassirer puts forward an idea that will be revisited in The Myth of the State and prevails in a good part of his works. Philosophy must be accountable for promoting certain political climates, such as what happened with some thinkers who favoured the consolidation of Nazism. Thought crises may generate social or political turbulences, because in these circumstances there is a continuous dialectic between thinkers and people of action, between ideas and facts, summing up, between theory and praxis. The main historic-political problems cannot be solved without taking into account the fundamental questions approached from a philosophical perspective, because there is an unavoidable interaction between the structure of ideas and our socio-political reality. The Davos’s debate, The idea of the Republican Constitution, The problem Jean-Jacques Rousseau and Moral Philosophy, Rights and Metaphysics: A dialogue with Axel Hägerstrom are presented in order to illustrate this thesis defended by the author of this paper, who has also written La Quimera del Rey Filósofo (The Chimera of the Philosopher King).[ES] En su conferencia de 1944 sobre Filosofía y Política Ernst Cassirer expone algo que será retomado por El mito del Estado y preside buena parte de su obra. La filosofía debe rendir cuentas en cuanto responsable indirecta de ciertos climas políticos, tal como sucedió con ciertos pensadores que propiciaron la consolidación del nazismo. Las crisis de pensamiento pueden generar convulsiones políticas o sociales, porque se da una continua dialéctica entre pensadores y hombres de acción, entre las ideas y los hechos, en definitiva, entre la teoría y la práctica. Los grandes problemas histórico-políticos no pueden resolverse sin atender a las cuestiones fundamentales abordadas desde una perspectiva filosófica, toda vez que se da una insoslayable interacción entre la estructura de las ideas y la configuración de nuestra realidad político-social. El debate de Davos, La idea de la constitución republicana, El problema Jean-Jacques Rousseau y Filosofía Moral, Derecho y Metafísica: Un diálogo con Axel Hägerstrom sirven para ilustrar esta tesis que hace suya el autor del artículo, que también lo es de La quimera del Rey FilósofoPeer reviewe
Philosophical Legacies of Traumas and Reveries in Rousseau, Kant and Schopenhauer
No full textIt could be said that Rousseau’s philosophical reflection was nourished by an original trauma, since his mother died as a result of childbirth a few days after his birth and he always felt guilty for that, even though such a circumstance contributed to design his conception of moral conscience. On the other hand, Rousseau not only wrote the Dreams of a Lonely Walker (1776) but also connected his own personal experiences with the literary characters of Julie, or the New Heloise (1761). Kant, the author of a visionary’s Dreams of a Ghost-seer explained by Dreams of Metaphysics (1765), said that without daytime dreamers such as Plato or Rousseau there would be no room for the moral progress of humanity. For his part, Schopenhauer was convinced that a premonitory dream had saved his life, making him leave Berlin so as not to fall victim to the same epidemic that killed Hegel. Schopenhauer understood that, by dreaming while we sleep, we access another universe where the space-time coordinates do not exist, on that other side of the Veil of Maya where we will return when we die and we were before we were born, coming to describe our ephemeral life as the dream of a primeval will that homologates with the thing in itself Kantian, making good what was said by his admired Calderon regarding that life is a dream. Curiously, Freud preferred to deny that he had read Schopenhauer, rather than recognize Schopenhauer's obvious influence on fundamental points of psychoanalysis, such as considering our dream life the best point of access to the unconscious, as shown by Leonardo da Vinci’s Childhood Memory (1910)Peer reviewe
Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae.
No full textInitiation factor eIF4G is a key regulator of eukaryotic protein synthesis, recognizing proteins bound at both ends of an mRNA to help recruit messages to the small (40S) ribosomal subunit. Notably, the genomes of a wide variety of eukaryotes encode multiple distinct variants of eIF4G. We found that deletion of eIF4G1, but not eIF4G2, impairs growth and global translation initiation rates in budding yeast under standard laboratory conditions. Not all mRNAs are equally sensitive to loss of eIF4G1; genes that encode messages with longer poly(A) tails are preferentially affected. However, eIF4G1-deletion strains contain significantly lower levels of total eIF4G, relative to eIF4G2-delete or wild type strains. Homogenic strains, which encode two copies of either eIF4G1 or eIF4G2 under native promoter control, express a single isoform at levels similar to the total amount of eIF4G in a wild type cell and have a similar capacity to support normal translation initiation rates. Polysome microarray analysis of these strains and the wild type parent showed that translationally active mRNAs are similar. These results suggest that total eIF4G levels, but not isoform-specific functions, determine mRNA-specific translational efficiency
Evaluating China's Presence in South America
No full textCHARLES UNIVERSITY IN PRAGUE FACULTY OF SOCIAL SCIENCES Institute of Political Studies Master Thesis 2020 Abril V. Mariaca CHARLES UNIVERSITY IN PRAGUE FACULTY OF SOCIAL SCIENCES Institute of Political Studies Abril V. Mariaca Evaluating China's Presence in South America Master Thesis Prague 2020 Author: Abril V. Mariaca Supervisor: Prof. Ing. Lourdes Daza Aramayo, PhD. Academic Year: 2019/2020 Abstract China is poised to become Latin America's largest trading partner and primary influence due to the steady rising of deals, economic financing, investments, and cultural exchanges implemented by China in the region. As such, China has used different tactics to ensure that it will continue to exert influence and gain access to strategic energy assets in the region. This thesis analyzes how Chinese engagement and presence has impacted South America's export basket. Consequently, China's presence has positioned Latin America back into a world of primary product dependency, limiting the development of high value-added exports, and adding consequences such as environmental and social conflicts across the region. The final section recommends proposals on how the region can better respond to and invest in the relationship, so that both China and Latin America can benefit from what is now an asymmetric relationship
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