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AutoDock Vina – simple example

Introduction In this exercise, we will perform a molecular docking simulation using AutoDock Vina to predict the binding orientation of a ligand within the binding site of a receptor protein. Molecular docking explores possible ligand conformations and orientations within a defined region of the receptor. AutoDock Vina evaluates these binding poses using a scoring function […]

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ENA Submission Guide

1. ๊ณ„์ • ์ƒ์„ฑ ๐Ÿ’ก ์ฐธ๊ณ : ๊ณ„์ •์ด ์Šน์ธ๋˜๋ฉด โ€œWebin IDโ€ (์˜ˆ: Webin-XXXXXX) ํ˜•ํƒœ์˜ ์‚ฌ์šฉ์ž๋ช…์ด ๋ฐœ๊ธ‰๋˜๋ฉฐ,์ดํ›„ ๋ชจ๋“  CLI ๋˜๋Š” ์›น ์ œ์ถœ ์‹œ ์ธ์ฆ์šฉ์œผ๋กœ ์‚ฌ์šฉ๋œ๋‹ค. 2. ์ž…๋ ฅ ์ ˆ์ฐจ ๊ฐœ์š” 3. Study ๋“ฑ๋ก ๐Ÿ’ก Study Accession์€ ์ดํ›„ Sample ๋ฐ Run ์ œ์ถœ ์‹œ ๋ฐ˜๋“œ์‹œ ํ•„์š”ํ•˜๋‹ค. 4. Sample ๋“ฑ๋ก ์ปฌ๋Ÿผ๋ช… ์„ค๋ช… tax_id Taxonomy id (์˜ˆ: 408170) project name Study ์ด๋ฆ„ (์˜ˆ: SNUH-IBD) sample_alias ๊ณ ์œ 

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Citing Literatures with Mendeley

Introduction Mendeley๋Š” Elsevier์—์„œ ์ œ๊ณตํ•˜๋Š” ์›น ๊ธฐ๋ฐ˜ ์„œ์ง€๊ด€๋ฆฌ ํ”„๋กœ๊ทธ๋žจ์ด์šฉ์ž๋Š” Mendeley๋ฅผ ํ†ตํ•ด ์„œ์ง€(Reference)๋ฅผ ์ˆ˜์ง‘ํ•˜๊ณ  ๊ด€๋ฆฌํ•˜๋ฉฐ, ๋…ผ๋ฌธ ์ž‘์„ฑ ์‹œ ์ˆ˜์ง‘ํ•œ ์„œ์ง€๋ฅผ ํŽธ๋ฆฌํ•˜๊ฒŒ ์ธ์šฉํ•  ์ˆ˜ ์žˆ์œผ๋ฉฐ, PC, ์Šค๋งˆํŠธํฐ ๋“ฑ์„ ์‚ฌ์šฉํ•ด ์–ด๋””์„œ๋‚˜ Mendeley Library์— ์ ‘๊ทผํ•  ์ˆ˜ ์žˆ์Šต๋‹ˆ๋‹ค. Mendeley์˜ ํ™”๋ฉด ๊ตฌ์„ฑ Mendeley ๊ณ„์ • ์ƒ์„ฑ ๋ฐ ์„ค์น˜ 5. ๋ฉ”์ธ ํ™”๋ฉด์œผ๋กœ ๋Œ์•„์™€ ํ™”๋ฉด ์šฐ์ธก ์ƒ๋‹จ์˜ “Download” ํด๋ฆญ 6. ์‚ฌ์šฉํ•˜๋Š” PC ์šด์˜์ฒด์ œ์— ๋งž๋Š” install

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Example – statistical test

JupyterNotebook (JupyterHub)์—์„œ ์•„๋ž˜ code๋ฅผ ์‹คํ–‰ํ•˜๋ฉด์„œ ํ†ต๊ณ„ ๋ถ„์„ ๊ณผ์ •์„ ์ดํ•ดํ•ฉ๋‹ˆ๋‹ค. Libraroy import ์ž„์˜ ๋ณ€์ˆ˜ ์ƒ์„ฑ ๋ณ€์ˆ˜ ๊ฐ’ ์‹œ๊ฐํ™” Pearson’s correlation test Normality tests Normality tests – QQ plot Normality tests – Shapiro-Wilk test Spearman’s correlation test (for non-normally distributed variable)

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Ubuntu ์„œ๋ฒ„ ๋น„๋ฐ€๋ฒˆํ˜ธ ๋ณ€๊ฒฝ

๋น„๋ฐ€๋ฒˆํ˜ธ ๋ณ€๊ฒฝ ๋ฐฉ๋ฒ• ์•„๋ž˜ ๋ช…๋ น์„ ์ด์šฉํ•˜์—ฌ ๋น„๋ฐ€๋ฒˆํ˜ธ๋ฅผ ๋ณ€๊ฒฝํ•  ์ˆ˜ ์žˆ๋‹ค. ๋จผ์ €, ์„ค์ •๋œ ๋น„๋ฐ€๋ฒˆํ˜ธ๋ฅผ ์ž…๋ ฅํ•˜๊ณ , ์ƒˆ๋กœ ์„ค์ •ํ•  ๋น„๋ฐ€๋ฒˆํ˜ธ๋ฅผ ์ž…๋ ฅํ•œ ํ›„ ์ƒˆ ๋น„๋ฐ€๋ฒˆํ˜ธ๋ฅผ ๋‹ค์‹œ ํ•œ๋ฒˆ ์ž…๋ ฅํ•˜์—ฌ ๋ณ€๊ฒฝํ•  ์ˆ˜ ์žˆ๋‹ค. ๋น„๋ฐ€๋ฒˆํ˜ธ ์ƒ์„ฑ ๊ทœ์น™ ํ•™๊ต ์„œ๋ฒ„์— ๋Œ€ํ•œ ํ•ดํ‚น ์‹œ๋„๊ฐ€ ๋งŽ์Šต๋‹ˆ๋‹ค. ๋‹ค์†Œ ๋ณต์žกํ•œ ๋น„๋ฐ€๋ฒˆํ˜ธ๋ฅผ ์„ค์ •ํ•ด์•ผ ํ•ฉ๋‹ˆ๋‹ค. ์•„๋ž˜์˜ ๊ทœ์น™์„ ๊ณ ๋ คํ•ฉ๋‹ˆ๋‹ค. ๊ฐœ์ธ์ ์ธ ์ •๋ณด๋ฅผ ์˜๋ฌธ์žํŒ์—์„œ ํ•œ๊ธ€๋กœ ์ž…๋ ฅํ•˜๋ฉด ์ข‹์Šต๋‹ˆ๋‹ค. ์•„๋ž˜ ์˜ˆ์‹œ๋Š” ์ผ๋ฐ˜์ ์ธ ๋‹จ์–ด๋ฅผ ์ด์šฉํ•œ

Ubuntu ์„œ๋ฒ„ ๋น„๋ฐ€๋ฒˆํ˜ธ ๋ณ€๊ฒฝ Read More ยป

๋ฐ์ดํ„ฐ๋ฒ ์ด์Šค ์‚ฌ์šฉ ์‹ค์Šต – FireProtDB

Introduction FireProtDB๋Š” ๋‹จ๋ฐฑ์งˆ ์—ด์•ˆ์ •์„ฑ์— ๋Œ€ํ•œ ์ •๋ณด๋ฅผ ์ˆ˜์ง‘ํ•˜๊ณ  ์ •๋ฆฌํ•œ ๋ฐ์ดํ„ฐ๋ฒ ์ด์Šค์ด๋‹ค. ์ด ๋ฐ์ดํ„ฐ ๋ฒ ์ด์Šค๋ฅผ ์ด์šฉํ•˜์—ฌ program (Python)์„ ์ด์šฉํ•œ ๋ฐ์ดํ„ฐ๋ฒ ์ด์Šค ์ ‘๊ทผ ๋ฐ ํ™œ์šฉ ๋ฐฉ๋ฒ•์„ ํ•™์Šตํ•œ๋‹ค. ์‹ค์Šต code ์•„๋ž˜ code๋Š” FireProtDB์— ์ ‘์†ํ•ด์„œ Tm ๊ฐ’๊ณผ ddG ๊ฐ’์„ ๊ฐ€์ ธ์˜ค๊ณ , ๊ฐ ๊ฐ’์˜ ๋ถ„ํฌ๋ฅผ ๋‚˜ํƒ€๋‚ด๋Š” ํ”„๋กœ๊ทธ๋žจ์ด๋‹ค. ์ด์™€ ๊ฐ™์ด ๋ฐ์ดํ„ฐ๋ฒ ์ด์Šค์™€ ํ”„๋กœ๊ทธ๋žจ์„ ์—ฐ๋™ํ•˜์—ฌ ๋ฐ์ดํ„ฐ ๋ถ„์„์„ ์ง„ํ–‰ํ•  ์ˆ˜ ์žˆ๋‹ค. 1. Load libraries ๋ฐ์ดํ„ฐ ๋ถ„์„์— ์‚ฌ์šฉํ•  ํ”„๋กœ๊ทธ๋žจ(library)๋ฅผ

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MobaXterm ์„ค์น˜์™€ ์„œ๋ฒ„ ์ ‘์†

Introduction MobaXterm์€ SSH client๋กœ ๋ฆฌ๋ˆ…์Šค ์‹œ์Šคํ…œ์— ์›๊ฒฉ ์ ‘์†ํ•˜๊ธฐ ์œ„ํ•ด ์‚ฌ์šฉํ•  ์ˆ˜ ์žˆ๋Š” ํ”„๋กœ๊ทธ๋žจ์ด๋‹ค.๋‹ค์Œ URL์„ ํ†ตํ•ด ํ™ˆํŽ˜์ด์ง€์— ์ ‘์†ํ•  ์ˆ˜ ์žˆ์œผ๋ฉฐ ์„ค์น˜ ํ”„๋กœ๊ทธ๋žจ์„ ๋ฐ›์„ ์ˆ˜ ์žˆ๋‹ค (https://mobaxterm.mobatek.net/). ๊ฐœ์ธ์  ํ™œ์šฉ์‹œ Home Edition์„ ์ด์šฉํ•˜์—ฌ ๋ฌด๋ฃŒ๋กœ ์‚ฌ์šฉํ•  ์ˆ˜ ์žˆ๋‹ค. ์„ค์น˜ ํ”„๋กœ๊ทธ๋žจ ๋ฐ›๊ธฐ ์•„๋ž˜ URL์—์„œ “Home Edition” ๋ฒ„์ „์„ ๋ฐ›๋Š”๋‹ค. (Download now) https://mobaxterm.mobatek.net/download.html (์ฐธ๊ณ ) ๊ฐœ์ธ ์ปดํ“จํ„ฐ์— ์„ค์น˜ํ•˜๋Š” ๊ฒฝ์šฐ installer edition๋ฅผ ์„ค์น˜ํ•œ๋‹ค. ๊ณต์šฉ

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