Fourth Kazan Summer School-Conference on Chemoinformatics (KSSCI2019)


TUTORIALS

For the tutorials we kindly ask you to use your own laptop. If you haven't possibility to use it, organizing committee could provide some limited number of laptops but please write corresponding letter to Scientific Secretary as soon as possible. To save your time, please install all required programs and download instructions prior to tutorials.

Please follow these instructions to prepare:

Tutorial on Molecular Dynamics, speaker - R. Stote

To participate in tutorial please install the programs: NAMD and VMD

1. NAMD: download program from web-page:

https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD.

NAMD Version 2.13 (2018-11-09)

Selecting an archive will lead to a user registration and login page. Your download will continue after you have registered or logged in.

Windows:

Win64 (Windows 7, 8, 10, etc.)

Linux:

Linux-x86_64 (64-bit Intel/AMD with ethernet)

MacOs:

MacOSX-x86_64 (Mac OS X for 64-bit Intel processors)

If you have portable computers with multiprocessors, installing mpi could be useful.

NB!: A NAMD binary distribution need only be untarred or unzipped and can be run directly in the resulting directory.

2. VMD: download program from web-page:

https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

VMD Version 1.9.3 (2016-11-30)

Windows:

Windows OpenGL (Microsoft Windows XP/Vista/7/8/10 (32-bit) using OpenGL)

Linux:

LINUX_64 OpenGL, CUDA, OptiX, OSPRay (Linux (RHEL 6.7 and later) 64-bit Intel/AMD x86_64 SSE, with CUDA 8.x, OptiX, OSPRay)

MacOs:

MacOS X OpenGL (32-bit Intel x86) (Apple MacOS-X (10.4.7 or later) with hardware OpenGL (native bundle))

Tutorial on Data processing, speaker - R. Nugmanov

To participate in tutorial please install the programs and the packages below.

I. PART 1

Linux Debian based

1. Install python3.7, virtualenv and git

sudo apt install python3.7 python3.7-dev git python3-virtualenv

2. Create new environment and activate it.

virtualenv -p python3.7 venv

source venv/bin/activate

MacOS

1. Download and install Homebrew – the instruction can be find on link: https://brew.sh/

2. Install python3.7 and git using Homebrew

brew install git

brew install python3

3. Install virtualenv.

pip install virtualenv

4. Create new environment and activate it.

virtualenv -p python3.7 venv

source venv/bin/activate

Windows

1. Download and install Chocolatey – the instruction can be find on link: https://chocolatey.org/

2. Install python3.7 and git using Chocolatey

choco install git

choco install python3

3. Install virtualenv.

pip install virtualenv

4. Create new environment and activate it.

virtualenv venv

venv\Scripts\activate

II. PART 2

General part (the same for Linux, MacOS and Windows)

Do this after first part installation.

1. Install CGRTools - stable version will be available through PyPI

pip install CGRTools

2. Jupyter integration:

pip install jupyter

jupyter notebook

3. Download tutorial files to same directory

Files for tutorial: download

Open .ipynb files from tutorial directory in Jupyter browser.

Last version of CGRtools: download