Lab Documentations

This is how we stand on the shoulders of giants

Lab Documentations

This is how we stand on the shoulders of giants

08-23-2023: Computational Skills for Plant Sciences

Resources to learn basic computational skills

Linux Command Lines edX: Learn Linux Command Line 1 hour Linux Commands & Shell Scripting 1 hour Git Best Practices Coursera: Getting Started with Git and GitHub Three modules (7 hours in total)... [Read More]

12-04-2019: Guidelines for The JYang Lab weekly report

Here you can find the template slides for your weekly report. Overall guidelines Submit to the Box folder LabPPT in a powerpoint format before the scheduled meeting time. Save as: Name_Month-Date-Year_key-words.pptx. For example: JYang_12-04-2019_linear-mixed-model.pptx. Include a title page... [Read More]

12-03-2019: The Laws of Herman for graduate students

Dr. Herman wrote a guide for the perplexed graduate student doing research. It is a piece of article I think that every graduate student should read. “Supervised research is a symbiotic (although not symmetric) interaction between student and adviser.” Here I copied the laws: The laws... [Read More]

09-06-2018: HCC Usage

The Holland Computing Center (HCC) provides the primary high performance computing resources for J. Yang lab. This document below serves as a reference for the most commonly used commands and workflows for the workload manager SLURM. This documentation borrowed much of its text from Ross-Ibarra... [Read More]

08-15-2017: Statistics Resources

Resources to learn basic statistics

Statistics Online Resources fiveMinuteStats Statistics Online Courses HarvardX Biomedical Data Science Open Online Training [Read More]

05-01-2017: Data Plans

Data storage, back-up, and sharing

Here we are talking about long-term storage for large amount of data. Below we list some solutions from private companies. But universities normally provide a more cost effective storage system/plan. STORAGE AMAZON S3 GOOGLE CLOUD GOOGLE DRIVE <th style="text-align:... [Read More]

01-10-2017: Using Github for a Collabrative Research Project

fork, pull, push, and pull request

Getting started with Git and GitHub, check this out. Here is the collaborative workflow: 1. Fork the project on Github to your own repo and Git clone or download source code. git clone git@github.com:YOUR_GITHUB_ID/PROJECT.github.io.git 2. Create... [Read More]

01-07-2017: The Best Practices for Project Management

Suggestions for a re-producible and productive research project

As computational/statistical researchers, we often found ourselves had a hard in finding data, codes or related notes. From several years of research experience, I experimented many note-taking and project management tools. Among those, I found the following practices are the most efficient and productive ones. Git controlled Of course,... [Read More]

01-04-2017: Essential Bioinformatic Resoures

Bio-info tools

FASTQ trimming and error correction FASTX-Tools: Filter and trim fastq files Quake: Error Correction of Short Reads Aligners and variant callers BWA: Feature rich short read aligner Bowtie: Ultra-fast short read mapping Picard: SAM/BAM alignment filtering SAMtools: SAM/BAM alignment... [Read More]

11-15-2016: Maize Genome Resources

RefGen and Annotation Information

Reference Genome: AGPv4: Gramene has refgen4 maize resources and annotations. AGPv4.33 GFF3 Previous releases (FTP site): release-3a.50 (2008-12) - Pre-assembly BAC-based gene build release-3b.50 (2009-02) - Pre-assembly BAC-based gene build + Filtered Gene Set release-4a.53 (2009-10) - Maize RefGen_v1 release-5a (2010-11)... [Read More]