Resources - XY-Lab

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An AI/computing platform for biomedical research, integrating lab-hosted compute and services, AI tools, and representative research outputs. -Launched in 2025 · Maintained by Yun Xia

面向“人工智能通识+生物信息学实践”教学，XY-Lab平台汇集并持续完善自研课程包、练习与作业模板、标准化实践流程和统一计算环境配置；同时展示实验室建设的数据库、分析工具与阶段性科研产出，并整合本地部署的常用AI与计算工具入口，为师生提供一站式访问、学习与实践导航。平台v1.0版本于2025年上线，目前已更新至v5.11版本，最近一次更新为2026年10月10日，由夏老师持续维护。

AI Platforms & Computing Tools

Teaching: RStudio Server

R & Bioconductor

Researching: RStudio Server

R & Bioconductor

XY-Lab Password Strength—Password security assessment and strength analysis tool

Evaluate password strength, security risks, and improve account protection

Teaching: JupyterHub

Notebooks & Kernels

Researching: JupyterHub

Notebooks & Kernels

Teaching: Student Administration

Teaching: Student Administration

Teaching2: Student Administration

Teaching2: Student Administration

Teaching: Virtualization Console

Proxmox VE Web Console

Researching: Virtualization Console

Proxmox VE Web Console

The elegant way to command your servers — anywhere

Run efficient multimodal AI with MiniCPM

Generate natural, lifelike cloned voices with AI

Generate expressive, natural speech with AI

A powerful AI creation platform

A visual gallery for exploring and managing AI-generated creations

Multi-model AI chat workspace for research and daily use

AI for biomolecular structure & interactions

XY-Lab -License—License management and activation console

License issuance, activation, and device binding in one place

XY-Lab Token Center—API token management and usage control console

API token management, model access, and usage control in one place

XY-Lab API Center—Unified API access and key management console

Manage API keys, model access, usage, and service endpoints in one place

Agent & Databases & Tools

FigFlow—Updating; service may be temporarily unavailable.

Al workflows for scientific figures.

plotXY Online— Updating; service may be temporarily unavailable.

Easy, fast, and beautiful online plotting by XY-Lab. No installation, no coding!

Transform your scripts into PlotXY tools anyone can use with our AI agent.

OmicsForge AI— Updating; service may be temporarily unavailable.

AI-assisted omics platform generation and bioinformatics tool development.

scTIMEcomb—Updating; service may be temporarily unavailable.

Your portal for exploring single-cell data of immune checkpoint inhibitor combination therapy

ParmPath—Updating; service may be temporarily unavailable.

A web platform for phenotype-guided signature mining and candidate drug screening.

plotXY ---GSEA—Updating; service may be temporarily unavailable.

Gene Set Enrichment Analysis in One Page

Pert Atlas—Updating; service may be temporarily unavailable.

A platform for exploring transcriptional responses to small molecules

An intelligent drug–target interaction prediction platform powered by hypergraph masked autoencoders

ICBcomb—under the guidance of Guo-Lab

Immune Checkpoint Blockade Combination Therapy

ICBcDrug—under the guidance of Guo-Lab

A database of ICB combination Drugs

ICB Booster X—Coming Soon!

ICB-enhancing Small Molecules & Gene site

XY-Lab Classes: AI Foundations — Linux Series

Linux: 1. Introduction

What Linux is, why it matters, and how it is used in bioinformatics

Linux: 2. Basic knowledge

CPU, GPU, RAM, ROM, storage, and basic data units

Linux: 3. Virtual Machine Software Installation

Download and install VMware Workstation Pro for course virtual machines

Linux: 4. Ubuntu installation for windows

Installing Ubuntu on Windows and avoiding common setup issues

Linux: 5. Ubuntu installation for mac

Running Ubuntu on macOS using virtualization tools

Linux: 6. Command line

Essential commands: files, paths, pipes, and basic text operations

RAID levels at a glance: combining multiple disks to improve performance, capacity, and/or fault tolerance

Linux: 8. Background & Parallel

nohup/disown, loops, GNU parallel, and xargs -P for safe batch jobs

Linux: 9. Environment Variables

env/export, startup files, and reproducible configs across sessions

Linux: 10. $PATH

Install pitfalls: wrong $PATH syntax, ordering, and “command not found” fixes

Linux: 11. Virtualization & Containers

VM vs container: images, isolation, volumes, networks, and common use cases

XY-Lab Classes: RNAseq Series

RNAseq: 1. Sequencing Evolution

Key milestones in sequencing technology evolution

RNAseq: 2. Illumina Sequencing Workflow

Step-by-step overview of Illumina library prep, sequencing, and data output

Secure, reproducible Python environments for AI with trusted packages

RNAseq: 3. Sequencing QC

Run quality checks on raw reads to detect issues early

RNAseq: 4. Sequencing QC Report

Interpret QC metrics and summarize results for troubleshooting

RNAseq: 5. Trimming

Remove adapters and low-quality bases to improve downstream accuracy

RNAseq: 6. Read Alignment

Map cleaned reads to a reference genome/transcriptome to locate their origin

RNAseq: 7. Gene Quantification

Count reads per gene/transcript to generate an expression matrix for analysis