The Carpentries comprende las comunidades de instructores, formadores, mantenedores, ayudantes y partidarios de Software Carpentry, Data Carpentry, y
Library Carpentry que comparten la misión de enseñar habilidades básicas de computación y ciencia de datos a los investigadores.
¿Quiere obtener más información y seguir interactuando con The Carpentries? Carpentries Clippings es el boletín quincenal de The Carpentries, donde compartimos noticias de la comunidad, ofertas de trabajo de la comunidad y más.
Regístrese para recibir ediciones futuras y leer nuestro archivo completo: https://carpentries.org/newsletter/
El laboratorio Nacional de Apoyo tecnologico a las ciencias Genomicas ( LNATCG), tiene como una de sus directrices la capacitación en areas de Bioinformatica y
Software Carpentry
tiene como objetivo ayudar a los investigadores a realizar su trabajo en menos tiempo y con menos esfuerzo enseñándoles habilidades informáticas básicas de investigación.
Este taller práctico cubrirá conceptos y herramientas básicos, incluido el diseño de programas, control de versiones, gestión de datos y automatización de tareas, que son tareas escenciales en la iniciación a la bioinformatica. Se alentará a los participantes a que se ayuden unos a otros y apliquen lo que hayan aprendido a sus propios problemas de investigación.
Para obtener más información sobre lo que enseñamos y por qué, consulte nuestro artículo:
"Best Practices for Scientific Computing". ("Mejores prácticas para la informática científica")
Para Quienes:
El curso está dirigido a estudiantes de posgrado y otros investigadores. No es necesario tener ningún conocimiento previo de las herramientas que se presentarán en el taller.
Donde: Esta formación se realizará online.
Los instructores le proporcionarán una liga de zoom con la información que necesitará para conectarse a esta reunión, via el correo electronico con el que se registre
Requerimientos:
Los participantes deben tener acceso a una computadora con
Sistema operativo Mac, Linux o Windows (no una tableta, Chromebook, etc.) con privilegios de administracion.
También es recomendable una velocidad de conexion a internet de al menos 3M (esto lo puede verificar en https://www.speedtest.net/ )
zoom para las videoconferencias, con su nombre completo definido como usuario al momento de conectarse a la sesión
Deben tener ademas, acceso a una terminal y tener instalado python y como sugerencia visual code (instrucciones abajo).
Accessibilidad:
Estamos dedicados a proporcionar un ambiente de aprendizaje positivo y accesible para todos.
No requerimos que los participantes proporcionen documentación de discapacidades ni revelen información personal innecesaria.
Sin embargo, queremos ayudar a crear una experiencia inclusiva y accesible para todos los participantes.
Le animamos a compartir cualquier información que pueda resultar útil para que su experiencia en Carpentries sea accesible.
Para solicitar una adaptación para este taller, complete el formulario
formulario de solicitud de adaptación.
Si tiene preguntas o necesita ayuda con el formulario de adaptacion, envíenos un correo electrónico.
¿Quien puede asistir?:
Este taller esta abierto al publico en general. Las solicitudes de inscripción se realizan llenado el siguiente formnulario La demanda al taller es muuy alta. Si por alguna razón te inscribiste y no puedes asistir, notificano, para poder dar cabida a las personas en la lista de espera.
Solicitud de inscripción
Codigo de conducta
Todos los que participan en las actividades de Carpentries deben cumplir con el Código de conducta. Este documento también describe cómo informar un incidente si es necesario.
Puedes revisar una version en español aquí
</p>
To participate in a
Software Carpentry
workshop,
you will need access to software as described below.
In addition, you will need an up-to-date web browser.
If you haven't used Zoom before, go to the
official website
to download and install the Zoom client for your computer.
Set up your workspace
Like other Carpentries workshops,
you will be learning by "coding along" with the Instructors.
To do this, you will need to have both the window for the tool
you will be learning about (a terminal, RStudio, your web browser, etc..)
and the window for the Zoom video conference client open.
In order to see both at once,
we recommend using one of the following set up options:
Two monitors: If you have two monitors,
plan to have the tool you are learning up on one monitor and
the video conferencing software on the other.
Two devices: If you don't have two monitors,
do you have another device (tablet, smartphone) with a medium to large
sized screen? If so, try using the smaller device as your video
conference connection and your larger device (laptop or desktop)
to follow along with the tool you will be learning about.
Divide your screen: If you only have one device
and one screen, practice having two windows
(the video conference program and one of the tools you will be using
at the workshop) open together.
How can you best fit both on your screen?
Will it work better for you to toggle between them
using a keyboard shortcut?
Try it out in advance to decide what will work best for you.
This blog post includes detailed information on how to set up your screen to follow along during the workshop.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do
tasks more quickly.
Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.
From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
On the page that says "Adjusting the name of the initial branch in new repositories", ensure that
"Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
Ensure that "Git from the command line and also from 3rd-party software" is selected and
click on "Next". (If you don't do this Git Bash will not work properly, requiring you to
remove the Git Bash installation, re-run the installer and to select the "Git from the
command line and also from 3rd-party software" option.)
Select "Use bundled OpenSSH".
Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
Ensure that "Use Windows' default console window" is selected and click on "Next".
Ensure that "Default (fast-forward or merge) is selected and click "Next"
Ensure that "Git Credential Manager" is selected and click on "Next".
Ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Click on "Finish" or "Next".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press Enter)
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press Enter, you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing Enter
This will provide you with both Git and Bash in the Git Bash program.
Video Tutorial
The default shell in Mac OS X Ventura and newer versions is Zsh, but
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL
in Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
Video Tutorial
The default shell is usually Bash and there is usually no need to
install anything.
To see if your default shell is Bash type echo $SHELL
in Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
Git
Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser.
You will need an account at github.com
for parts of the Git lesson. Basic GitHub accounts are free. We encourage
you to create a GitHub account if you don't have one already.
Please consider what personal information you'd like to reveal. For
example, you may want to review these
instructions
for keeping your email address private provided at GitHub.
For macOS, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
Video Tutorial
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.
Text Editor
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+Q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.
Video Tutorial
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
Python
Python is a popular language for
research computing, and great for general-purpose programming as
well. Installing all of its research packages individually can be
a bit difficult, so we recommend
Anaconda,
an all-in-one installer.
Regardless of how you choose to install it,
please make sure you install Python version 3.x
(e.g., 3.6 is fine).
We will teach Python using the Jupyter Notebook,
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all
supported
(some older browsers, including Internet Explorer version 9
and below, are not).
Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
Download the Anaconda Installer with Python 3 for Linux.
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
Open a terminal window and navigate to the directory where
the executable is downloaded (e.g., `cd ~/Downloads`).
Type
bash Anaconda3-
and then press
Tab to autocomplete the full file name. The name of
file you just downloaded should appear.
Press Enter
(or Return depending on your keyboard).
You will follow the text-only prompts.
To move through the text, press Spacebar.
Type yes and press enter to approve the license.
Press Enter (or Return)
to approve the default location
for the files.
Type yes and press
Enter (or Return)
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).