How to Access Ubuntu via Remote Desktop from Windows
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https://phoenixnap.com/kb/ubuntu-remote-desktop-from-windows
XRDP Desktop does not look same as Ubuntu Desktop
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https://askubuntu.com/questions/1298907/xrdp-desktop-does-not-look-same-as-ubuntu-desktop
Prevent Ubuntu from changing hardware clock
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https://askubuntu.com/questions/963132/prevent-ubuntu-from-changing-hardware-clock
System parameters: CPU, RAM & so on
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sudo lshw | more # scroll dow to find RAM Type
sudo dmidecode -t 16 # show max RAM capacity
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// https://www.cgl.ucsf.edu/chimerax/download.html
sudo dpkg -i ucsf-chimerax_1.7.1ubuntu22.04_amd64.deb # to install
-- installation failed. So I did command below and reainstalled once again
sudo apt update && sudo apt upgrade
sudo apt --fix-broken install
sudo dpkg -r ucsf-chimerax # to remove
sudo dpkg -i ucsf-chimerax_1.7.1ubuntu22.04_amd64.deb # to install
-- 2024-02-19
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dowmload JDK:
(visit) https://www.oracle.com/ca-en/java/technologies/downloads/
(Look for "x64 Debian Package" & click on)
https://download.oracle.com/java/21/latest/jdk-21_linux-x64_bin.deb (sha256)
(that will download) jdk-21_linux-x64_bin.deb
To install the 64-bit JDK Debian package on a Linux platform:
(term) cd /home/laura/Downloads
(term) sudo dpkg -i jdk-21_linux-x64_bin.deb
Verify installation
(term) java --version
(shoujava 21.0.2 2024-01-16 LTS
Java(TM) SE Runtime Environment (build 21.0.2+13-LTS-58)
Java HotSpot(TM) 64-Bit Server VM (build 21.0.2+13-LTS-58, mixed mode, sharing)
(should see something like)
- java 21.0.2 2024-01-16 LTS
- Java(TM) SE Runtime Environment (build 21.0.2+13-LTS-58)
- Java HotSpot(TM) 64-Bit Server VM (build 21.0.2+13-LTS-58, mixed mode, sharing)
Delete the .deb file if you want to save disk space
(term) cd /home/laura/Downloads
(term) rm jdk-21_linux-x64_bin.deb
The Java Development Kit files are installed into /usr/lib/jvm/jdk--oracle- directory. For example, JDK 21 releases for x64 will be installed in /usr/lib/jvm/jdk-21-oracle-x64 directory.
https://netbeans.apache.org/front/main/download/nb21/
I downloaded: apache-netbeans_21-1_all.deb
sudo dpkg -i apache-netbeans_21-1_all.deb
-- 2024-02-28
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https://www.eclipse.org/downloads/packages/
I downloaded: Eclipse IDE for Enterprise Java and Web Developers (Linux x86_64)
(eclipse-jee-2023-12-R-linux-gtk-x86_64.tar.gz)
cd /home/rick/Local
mkdir Eclipse
cd Eclipse
cp /home/rick/Download/eclipse-jee-2023-12-R-linux-gtk-x86_64.tar.gz ./.
tar xfv eclipse-jee-2023-12-R-linux-gtk-x86_64.tar.gz
https://askubuntu.com/questions/1082340/how-to-add-eclipse-to-favorites
Eclipse Download and Installation (for Python) Instructions>
https://ics.uci.edu/~pattis/common/handouts/pythoneclipsejava/eclipsepython.html
Note: Start Eclipse, Start URL in Browser, Find "7. Click Help (on the far right ..." and follow the instructions.
-- 2024-02-29
ProDy: Protein Dynamic & Sequence Analysis
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http://prody.csb.pitt.edu/
sudo apt install python3-pip ### to install pip
sudo pip install prody ### To install ProDy
Note: I installed but did not try it yet.
VMD: How to install VMD on Ubuntu?
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https://bioinformaticsreview.com/20220301/how-to-install-vmd-on-ubuntu/
I downloaded: vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz
I accepted all default settings at config.
The last comand was: "sudo make install". You do not need the further commands.
(type in term) vmd (to start viewer)
LigthDock (on Ubuntu, my laptop)
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https://server.lightdock.org/ (web server - works with small files only)
(download) url = https://lightdock.org/
I downloaded: lightdock-0.9.4.tar.gz
tar xzvf lightdock-0.9.4.tar.gz
cd lightdock-0.9.4
(read) READ.md (for installation instructions)
sudo pip install lightdock (that compiled all dependencies)
(to test use):
Simple protein-protein docking example
https://lightdock.org/tutorials/0.9.3/simple_docking
on IJCluster
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https://numdifftools.readthedocs.io/en/stable/how-to/create_virtual_env_with_conda.html
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How to create virtual environments for python with conda
conda info --envs # # list enviroments
conda remove -n yourenvname -all # delete virtual env
conda info # the first line is the currently active env
# create environment
conda -V # version
conda update conda # update to the latest
conda search "^python$" # to see the list of available python versions
conda create -n yourenvname python=x.x anaconda # template
conda create -n ligthdock python=3.10.12 anaconda # the command I used
https://lightdock.org/tutorials/0.9.3/simple_docking # to run test
conda activate ligthdock
python --version # Python 3.10.12
pip --version # pip --version
pip install lightdock
pip install FuzzyTM
pip install gensim
conda deactivate
-- end of LightDock on IJCluster --------------------------------------