https://chk.ipmb.sinica.edu.tw/wiki/ 2026-04-19T16:54:49+00:00 https://chk.ipmb.sinica.edu.tw/wiki/ https://chk.ipmb.sinica.edu.tw/wiki/lib/exe/fetch.php/wiki/logo.png text/html 2026-02-09T02:54:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/ai_llm_tools?rev=1770605645&do=diff AI/LLM Tools About * A brief guide to using large language models (LLMs) often referred to as artificial intelligence (AI) tools, such as ChatGPT by OpenAI and Gemini by Google, in the context of academic research and writing. By Chih-Horng Kuo (chk@gate.sinica.edu.tw). Suggestions are welcome. text/html 2012-11-23T05:59:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/bash?rev=1353650388&do=diff Bash Sample configuration files and useful commands. Sample Configuration Files .bash_profile # .bash_profile # Get the aliases and functions if [ -f ~/.bashrc ]; then . ~/.bashrc fi .bashrc (Mac OS X) # .bashrc # User specific aliases and functions # set prompt, format = 'user@host[pwd]$ ', for example: 'chkuo@oak[~]$ ' PS1='\[\e[1;34m\]\u\[\e[0m\]\[\e[1;33m\]@\[\e[0m\]\[\e[1;31m\]\h\[\e[0m\][\w]\[\e[1;32m\]\$\[\e[0m\] ' # User specific environment and startup programs export … text/html 2024-01-02T14:32:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/cv?rev=1704205956&do=diff Curriculum Vitae (CV) * A brief guide on preparing a curriculum vitae (CV) for your academic career; by Chih-Horng Kuo (chk@gate.sinica.edu.tw) * Target audience: undergraduate students, graduate students, and postdocs (in biology) Considerations text/html 2025-06-08T14:33:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/faculty_jobs?rev=1749393199&do=diff Faculty Jobs * A brief guide on how to get a faculty job; by Chih-Horng Kuo (chk@gate.sinica.edu.tw) * The information here mostly reflects the opinion and experience of one person * Remember: during the process, your application needs to pass several round of votes (e.g., recruitment committee and department faculty). In each round, there is a group of potentially diverse people, and every vote counts. text/html 2025-09-09T12:05:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/file_management?rev=1757419520&do=diff File Management * Guidelines that Chih-Horng Kuo (chk@gate.sinica.edu.tw) developed for our group members. Suggestions are welcome. * Related information: * Scientific Presentations * Scientific Writing Backup * Critical! * File loss happens. Not IF, but WHEN. * Establish an automatic backup plan; manual backup plans are not practical text/html 2025-09-15T09:42:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/group_chat?rev=1757929352&do=diff Group Chat Introduction * Group chat tools (e.g., Google Chat, Mattermost, Slack, Discord) can be highly effective for team communication * Concept: a platform for work-related communication; no notification outside of working hours. * Email: for external and formal communication text/html 2012-01-21T17:25:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/learning_linux?rev=1327166735&do=diff Learning Linux Objectives * Learn about the filesystem * Absolute path versus relative path * The '/' (root) and '~/' (home) directory * File/directory ownership and permissions * Learn about the Bourne-again shell (Bash) and basic shell commands text/html 2010-10-06T16:43:52+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/learning_perl?rev=1286383432&do=diff Learning Perl Objectives * Read and understand chapters 1-13 in Learning Perl. * Perl quick reference * Know how to write some simple scripts. For example, solve all (or at least most) of the problems in the perl exercise page. * Know how to use standard modules. For example, text/html 2023-10-03T05:03:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/linux_essential_commands?rev=1696309420&do=diff Linux Essential Commands * man: manual page. * Explains how to use a shell command. * man <COMMAND>: For example, to find out how to use man, type man man * ls: list directory content * cd: change directory * pwd: print working directory text/html 2012-03-01T06:02:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl_cpan?rev=1330581763&do=diff Using the Comprehensive Perl Archive Network (CPAN) CPAN * CPAN is a large collection of perl modules. Installing modules To call the CPAN shell interface, use: $ sudo perl -MCPAN -e shell Using sudo allows for system-wide installation of new modules. When the call is successful, you should see a shell interface: text/html 2017-04-12T09:27:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl_examples?rev=1491989231&do=diff Perl examples * Find empty files in a directory: find_empty_file.2.pl * Rename files based on regex: rename_file_by_regex.3.pl * Generate command scripts to run blast+: cmd_blast+.1.pl * Execute command scripts: execute.3.pl * Parse blast+ results, 1 hit per line: parse_blast_sim.6.pl * Parse blast+ results, 1 HSP per line: parse_blast_hsp.4.pl text/html 2010-08-06T16:42:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl_exercises?rev=1281112933&do=diff Perl Exercises read_and_write Read from an input file and write the content to an output file. Assume the two filenames are provided in the command line. Hint: learn about filehandle before attempting this exercise. $ cat input.txt George Washington John Adams Thomas Jefferson James Madison James Monroe $ perl read_and_write.pl input.txt output.txt $ cat output.txt George Washington John Adams Thomas Jefferson James Madison James Monroe text/html 2018-12-19T02:59:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl_quick_reference?rev=1545188370&do=diff Perl Quick Reference * ($): variable is a name for a container that holds one or more values; use $ to get the value. * (!): negation operator * (tr): transliterating one group of characters into another. * (s): substitution * (%): modulus operator: text/html 2016-01-05T16:54:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/permission?rev=1452012849&do=diff Permission Tricks * recursive chmod * see <http://superuser.com/questions/91935/how-to-chmod-all-directories-except-files-recursively/91966> * find /path/to/base/dir -type d -print0 | xargs -0 chmod 755 * find /path/to/base/dir -type f -print0 | xargs -0 chmod 644 text/html 2022-06-21T04:00:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/regression_excel?rev=1655784057&do=diff Regression analysis in Excel Excel is not a program designed for statistical analysis, although it comes in handy when all you want to do is some quick and dirty analyses. However, you should be cautious about the results, as some can be simply wrong. Here is one problem from my experience with Office 2008 for Mac. text/html 2019-01-11T09:35:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/remote_access?rev=1547199336&do=diff Remote access SSH Login ssh (SSH client) is a program for logging into a remote machine. The typical usage is ssh user@hostname, for example: ssh jake@168.192.1.1 If the username is the same in the two machines (i.e., the local workstation and the remote server), the username can be omitted: text/html 2012-06-14T17:18:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/rsync?rev=1339694328&do=diff rsync rsync is a powerful tool for syncing files, either locally on the same machine or remotely between different machines. Use man rsync to read the manual pages to learn more. Examples If I want to sync (i.e., update all files that have been newly created or modified and remove all files that have been deleted) the text/html 2022-06-21T04:00:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/r_tips?rev=1655784003&do=diff R Tips General Tutorials * Quick-R: <http://www.statmethods.net/index.html> Read Data # assumes the input_file is a tab-delim text file with header row > dataset <- read.table("input_file", sep="\t", header=TRUE) # examine the dataset > summary(dataset) Regression Analysis Correlation text/html 2025-06-06T18:38:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/scientific_presentation?rev=1749235091&do=diff Scientific Presentations * Guidelines that Chih-Horng Kuo (chk@gate.sinica.edu.tw) developed for our group members. Suggestions are welcome. * Related information: * File Management * Scientific Writing General * Presenting your work, either through oral or poster presentations, provides excellent opportunities for you to think about your work critically, to examine the logic, to establish the context and a story line, and to prepare for writing. Also, such opportunities allow ot… text/html 2025-09-15T14:18:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/scientific_writing?rev=1757945910&do=diff Scientific Writing * Guidelines that Chih-Horng Kuo (chk@gate.sinica.edu.tw) developed for our group members. Suggestions are welcome. * Related information: * File Management * Scientific Presentations General * Writing is possibly the most important, yet also the most challenging part, of our work text/html 2025-06-08T16:17:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/start?rev=1749399474&do=diff Tutorials * Skills useful for academic and other careers * File management * AI/LLM tools * Scientific presentations * Scientific writing * CV: How to prepare a curriculum vitae? * Faculty jobs: How to get a faculty job? * Web tools: Twitter, online profiles, and others * Group chat: Using group chat (Mattermost) for team communication text/html 2025-09-15T02:44:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/web_tools?rev=1757904240&do=diff Web Tools Online Profiles * ORCID (Open Researcher and Contributor ID) * <https://orcid.org/> * Work, education, publication; simplified CV * Used by many journals to identify authors * Strongly recommended for people interested in an academic career *