ABI Knowledge Base

cluster_basics - [Network & Connectivity]

av (av@undisclosed.example.com) — 2026-04-08T00:36:16+00:00

Cluster Basics This page describes ABI's computing infrastructure at a level suitable for researchers. For detailed system administration documentation, see Infrastructure. What is an HPC Cluster? A High-Performance Computing (HPC) cluster is a collection of interconnected computers (called

support - created support page

av (av@undisclosed.example.com) — 2026-04-08T00:28:40+00:00

Support & Contact How to Get Help I need... What to do An account on the cluster Email it-support@abi.am with your name, email, and SSH public key. See New Member Onboarding. Software installed on the cluster Email it-support@abi.am with the tool name, version, and homepage. Or install it yourself with Conda. Help with Slurm / running jobs

start - updated projects page

av (av@undisclosed.example.com) — 2026-04-08T00:27:51+00:00

Research Projects This section documents ongoing and past research projects at ABI. Each project has its own page with details about goals, team members, data locations, and analysis methods. Active Projects Project Description Lead Status cfDNA Cell-free DNA analysis

start - created pipelines

av (av@undisclosed.example.com) — 2026-04-08T00:26:47+00:00

Bioinformatics Pipelines This section documents end-to-end bioinformatics workflows used at ABI. Each pipeline page describes a complete workflow from raw data to results, including the tools, scripts, and parameters used. For individual reusable scripts, see the

servers - created servers page

av (av@undisclosed.example.com) — 2026-04-08T00:25:08+00:00

Server Inventory This page lists all physical hosts and virtual machines in ABI's infrastructure. Physical Hosts All physical hosts run FreeBSD. Hostname Alias(es) Role OS CPU Sockets x Cores RAM Storage Notes geonosis nas0, genomic HPC hypervisor + NAS

overview - created overview

av (av@undisclosed.example.com) — 2026-04-08T00:23:35+00:00

Infrastructure Overview This page provides a high-level overview of ABI's computing and network infrastructure. For user-facing documentation, see Cluster Basics. Architecture ABI's infrastructure runs on FreeBSD physical hosts with compute workloads running in

changelog - created changelog

av (av@undisclosed.example.com) — 2026-04-08T00:19:16+00:00

Infrastructure Changelog This page documents changes to ABI's infrastructure -- server updates, software installations, configuration changes, maintenance events, and outages. Entries are in reverse chronological order (newest first). IT team: please add an entry here whenever you make a significant change.

wiki_editing - created wiki help page

av (av@undisclosed.example.com) — 2026-04-08T00:16:00+00:00

How to Edit This Wiki This wiki is powered by DokuWiki. It is an open platform where ABI members can contribute documentation. Currently, editing does not require logging in -- this may change in the future. Creating a New Page There are two ways to create a new page:

start - created database page; needs to be audited

av (av@undisclosed.example.com) — 2026-04-08T00:14:43+00:00

Databases & Reference Data ABI maintains a collection of reference genomes, indexes, and shared databases for use in bioinformatics analyses. These are stored on shared storage and are read-only for regular users. Location All shared databases are located under:

conda - created Conda page

av (av@undisclosed.example.com) — 2026-04-08T00:12:10+00:00

Installing Software with Conda Conda (via Miniconda) lets you install and manage software in your own user space without needing admin access. This is the recommended way to install tools that are not available system-wide. When to Use Conda * You need a tool that is not installed on the cluster.

slurm - created Slurm page

av (av@undisclosed.example.com) — 2026-04-08T00:10:33+00:00

Using Slurm Slurm (Simple Linux Utility for Resource Management) is the job scheduler on ABI's cluster. All compute jobs must be submitted through Slurm -- do not run heavy computation on the login nodes (ssh-01, ssh-02). ABI Partitions Partition

start - created Software page

av (av@undisclosed.example.com) — 2026-04-08T00:08:26+00:00

Software This section documents the software available on ABI's computing infrastructure, how to use it, and how to install your own tools. How Software is Managed All commonly used bioinformatics tools are installed globally on the cluster and available to all users. There is no module system

start

av (av@undisclosed.example.com) — 2026-04-08T00:04:57+00:00

Getting Started This section helps you get up and running at ABI, whether you are a new team member, a visiting researcher, or an IT staff member. New to ABI? Follow these guides in order: * New Member Onboarding -- Get your account, connect via SSH, and log in for the first time.

new_member - created new member page

av (av@undisclosed.example.com) — 2026-04-07T23:14:22+00:00

New Member Onboarding Welcome to ABI! This guide walks you through everything you need to do to get started as a new member. Overview Step What Time 1 Set up SSH 10 minutes 2 Request an account 10 minutes with 1 business day response time

start - Improved front page

av (av@undisclosed.example.com) — 2026-04-07T23:01:21+00:00

ABI Knowledge Base Welcome to the Armenian Bioinformatics Institute Knowledge Base -- the central hub for documentation, guides, and reference material for researchers and staff. ---------- Quick Links New Member? Start Here Submit a Job (Slurm) Get Support Cluster Basics Available Software Databases & Reference Genomes ---------- For Researchers

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av (av@undisclosed.example.com) — 2025-03-10T10:29:57+00:00

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av (av@undisclosed.example.com) — 2025-03-06T09:08:05+00:00

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av (av@undisclosed.example.com) — 2025-03-06T09:05:15+00:00