From 86c389747bf41de3e85e92a15bb77cf64dd8a84f Mon Sep 17 00:00:00 2001 From: 3mmaRand <7593411+3mmaRand@users.noreply.github.com> Date: Sat, 7 Oct 2023 10:59:04 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=203mmaRand?= =?UTF-8?q?/BIO00088H-data@8f8fe6797e26812600b29b16533459e3b3fb6eff=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- core/week-2/workshop.html | 58 ++++++++++++------------- omics/week-3/study_before_workshop.html | 22 +++++++--- search.json | 17 +++++--- 3 files changed, 58 insertions(+), 39 deletions(-) diff --git a/core/week-2/workshop.html b/core/week-2/workshop.html index 636f1bb..5a21467 100644 --- a/core/week-2/workshop.html +++ b/core/week-2/workshop.html @@ -425,15 +425,15 @@

Workshop

ls -l
total 136
-drwxr-xr-x 2 runner docker  4096 Oct  7 10:34 data
-drwxr-xr-x 2 runner docker  4096 Oct  7 10:34 images
--rw-r--r-- 1 runner docker  1597 Oct  7 10:34 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct  7 10:34 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 69876 Oct  7 10:37 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Oct  7 10:34 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct  7 10:34 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  8550 Oct  7 10:34 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Oct  7 10:37 workshop.rmarkdown
+drwxr-xr-x 2 runner docker 4096 Oct 7 10:56 data +drwxr-xr-x 2 runner docker 4096 Oct 7 10:56 images +-rw-r--r-- 1 runner docker 1597 Oct 7 10:56 overview.qmd +-rw-r--r-- 1 runner docker 184 Oct 7 10:56 study_after_workshop.qmd +-rw-r--r-- 1 runner docker 69876 Oct 7 10:58 study_before_workshop.html +-rw-r--r-- 1 runner docker 4807 Oct 7 10:56 study_before_workshop.ipynb +-rw-r--r-- 1 runner docker 13029 Oct 7 10:56 study_before_workshop.qmd +-rw-r--r-- 1 runner docker 8550 Oct 7 10:56 workshop.qmd +-rw-r--r-- 1 runner docker 8564 Oct 7 10:58 workshop.rmarkdown

You can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:

@@ -441,15 +441,15 @@

Workshop

ls -hl
total 136K
-drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 data
-drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 images
--rw-r--r-- 1 runner docker 1.6K Oct  7 10:34 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  7 10:34 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  7 10:37 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  7 10:34 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  7 10:34 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:34 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:37 workshop.rmarkdown
+drwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 data +drwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 images +-rw-r--r-- 1 runner docker 1.6K Oct 7 10:56 overview.qmd +-rw-r--r-- 1 runner docker 184 Oct 7 10:56 study_after_workshop.qmd +-rw-r--r-- 1 runner docker 69K Oct 7 10:58 study_before_workshop.html +-rw-r--r-- 1 runner docker 4.7K Oct 7 10:56 study_before_workshop.ipynb +-rw-r--r-- 1 runner docker 13K Oct 7 10:56 study_before_workshop.qmd +-rw-r--r-- 1 runner docker 8.4K Oct 7 10:56 workshop.qmd +-rw-r--r-- 1 runner docker 8.4K Oct 7 10:58 workshop.rmarkdown

The -a option stands for “all” and shows us all the files, including hidden files.

@@ -457,17 +457,17 @@

Workshop

ls -alh
total 144K
-drwxr-xr-x 4 runner docker 4.0K Oct  7 10:37 .
-drwxr-xr-x 5 runner docker 4.0K Oct  7 10:36 ..
-drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 data
-drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 images
--rw-r--r-- 1 runner docker 1.6K Oct  7 10:34 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  7 10:34 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  7 10:37 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  7 10:34 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  7 10:34 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:34 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:37 workshop.rmarkdown
+drwxr-xr-x 4 runner docker 4.0K Oct 7 10:58 . +drwxr-xr-x 5 runner docker 4.0K Oct 7 10:58 .. +drwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 data +drwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 images +-rw-r--r-- 1 runner docker 1.6K Oct 7 10:56 overview.qmd +-rw-r--r-- 1 runner docker 184 Oct 7 10:56 study_after_workshop.qmd +-rw-r--r-- 1 runner docker 69K Oct 7 10:58 study_before_workshop.html +-rw-r--r-- 1 runner docker 4.7K Oct 7 10:56 study_before_workshop.ipynb +-rw-r--r-- 1 runner docker 13K Oct 7 10:56 study_before_workshop.qmd +-rw-r--r-- 1 runner docker 8.4K Oct 7 10:56 workshop.qmd +-rw-r--r-- 1 runner docker 8.4K Oct 7 10:58 workshop.rmarkdown

You can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:

diff --git a/omics/week-3/study_before_workshop.html b/omics/week-3/study_before_workshop.html index a66f001..5f714d6 100644 --- a/omics/week-3/study_before_workshop.html +++ b/omics/week-3/study_before_workshop.html @@ -417,8 +417,8 @@

🐸 Aim

@@ -453,7 +453,7 @@

🐭 Experimental design

Schematic of stem cell experiment

@@ -464,7 +464,7 @@

🐭 Aim

@@ -494,12 +494,24 @@

Raw Sequence data

  • Short-read technologies e.g. Illumina have higher base accuracy but are harder to align
  • Long-read technologies e.g. Nanopore have lower base accuracy but are easier to align
    • + + + +
    +
    +

    The raw data

    + +
    +
    +

    Raw Sequence data

    +
    +
    -
    +

    Raw Sequence data

      diff --git a/search.json b/search.json index 3c466b9..d8f14db 100644 --- a/search.json +++ b/search.json @@ -361,7 +361,7 @@ "href": "omics/week-3/study_before_workshop.html#aim", "title": "Independent Study to prepare for workshop", "section": "🐸 Aim", - "text": "🐸 Aim\n\n\nfind genes important in frog development\nImportant means genes that are differentially expressed between the control and the FGF treated sibling\nDifferentially expressed means the expression on one group is significantly higher than the other" + "text": "🐸 Aim\n\n\nfind genes important in frog development\nImportant means the genes that are differentially expressed between the control-treated and the FGF-treated siblings\nDifferentially expressed means the expression in one group is significantly higher than in the other" }, { "objectID": "omics/week-3/study_before_workshop.html#guided-analysis", @@ -389,14 +389,14 @@ "href": "omics/week-3/study_before_workshop.html#experimental-design-6", "title": "Independent Study to prepare for workshop", "section": "🐭 Experimental design", - "text": "🐭 Experimental design\n\nSchematic of stem cell experiment\n\nThere are three cell types: LT-HSCs, HSPCs, Progs These are the “treaments”\nMany cells of each cell type were sequenced: These are the replicates\n155 LT-HSCs, 701 HSPCs, 798 Progs" + "text": "🐭 Experimental design\n\nSchematic of stem cell experiment\n\nThere are three cell types: LT-HSCs, HSPCs, Progs These are the “treaments”\nMany cells of each type were sequenced: These are the replicates\n155 LT-HSCs, 701 HSPCs, 798 Progs" }, { "objectID": "omics/week-3/study_before_workshop.html#aim-1", "href": "omics/week-3/study_before_workshop.html#aim-1", "title": "Independent Study to prepare for workshop", "section": "🐭 Aim", - "text": "🐭 Aim\n\n\nfind genes for cell surface proteins that are important in stem cell identity\nImportant means genes that are differentially expressed between at least two cell types\nDifferentially expressed means the expression on one group is significantly higher than the other" + "text": "🐭 Aim\n\n\nfind genes for cell surface proteins that are important in stem cell identity\nImportant means genes that are differentially expressed between at least two cell types\nDifferentially expressed means the expression in one group is significantly higher than in the other" }, { "objectID": "omics/week-3/study_before_workshop.html#guided-analysis-1", @@ -410,13 +410,20 @@ "href": "omics/week-3/study_before_workshop.html#raw-sequence-data", "title": "Independent Study to prepare for workshop", "section": "Raw Sequence data", - "text": "Raw Sequence data\n\n\nThe raw data are “reads” from a sequencing machine.\nA read is sequence of DNA or RNA shorter than the whole genome or transcriptome\nThe length of the reads depends on the type of sequencing machine\n\nShort-read technologies e.g. Illumina have higher base accuracy but are harder to align\nLong-read technologies e.g. Nanopore have lower base accuracy but are easier to align\n\nSequencing technology is constantly improving\nOptional: You can read more about Sequencing technologies in Statistically useful experimental design (Rand and Forrester 2022)" + "text": "Raw Sequence data\n\n\nThe raw data are “reads” from a sequencing machine.\nA read is sequence of DNA or RNA shorter than the whole genome or transcriptome\nThe length of the reads depends on the type of sequencing machine\n\nShort-read technologies e.g. Illumina have higher base accuracy but are harder to align\nLong-read technologies e.g. Nanopore have lower base accuracy but are easier to align" }, { "objectID": "omics/week-3/study_before_workshop.html#raw-sequence-data-1", "href": "omics/week-3/study_before_workshop.html#raw-sequence-data-1", "title": "Independent Study to prepare for workshop", "section": "Raw Sequence data", + "text": "Raw Sequence data\n\n\nSequencing technology is constantly improving\nOptional: You can read more about Sequencing technologies in Statistically useful experimental design (Rand and Forrester 2022)" + }, + { + "objectID": "omics/week-3/study_before_workshop.html#raw-sequence-data-2", + "href": "omics/week-3/study_before_workshop.html#raw-sequence-data-2", + "title": "Independent Study to prepare for workshop", + "section": "Raw Sequence data", "text": "Raw Sequence data\n\n\nThe RNA-seq data are from an Illumina machine 150-300bp; Metagenomic data are often Nanopore 10,000 - 30000bp\nReads are in FASTQ files\nFASTQ files contain the sequence of each read and a quality score for each base" }, { @@ -613,7 +620,7 @@ "href": "core/week-2/workshop.html#rstudio-terminal", "title": "Workshop", "section": "RStudio terminal", - "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like > on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.html\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.qmd\nworkshop.rmarkdown\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 136\ndrwxr-xr-x 2 runner docker 4096 Oct 7 10:34 data\ndrwxr-xr-x 2 runner docker 4096 Oct 7 10:34 images\n-rw-r--r-- 1 runner docker 1597 Oct 7 10:34 overview.qmd\n-rw-r--r-- 1 runner docker 184 Oct 7 10:34 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69876 Oct 7 10:37 study_before_workshop.html\n-rw-r--r-- 1 runner docker 4807 Oct 7 10:34 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Oct 7 10:34 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 8550 Oct 7 10:34 workshop.qmd\n-rw-r--r-- 1 runner docker 8564 Oct 7 10:37 workshop.rmarkdown\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 136K\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:34 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:34 images\n-rw-r--r-- 1 runner docker 1.6K Oct 7 10:34 overview.qmd\n-rw-r--r-- 1 runner docker 184 Oct 7 10:34 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69K Oct 7 10:37 study_before_workshop.html\n-rw-r--r-- 1 runner docker 4.7K Oct 7 10:34 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Oct 7 10:34 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:34 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:37 workshop.rmarkdown\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 144K\ndrwxr-xr-x 4 runner docker 4.0K Oct 7 10:37 .\ndrwxr-xr-x 5 runner docker 4.0K Oct 7 10:36 ..\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:34 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:34 images\n-rw-r--r-- 1 runner docker 1.6K Oct 7 10:34 overview.qmd\n-rw-r--r-- 1 runner docker 184 Oct 7 10:34 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69K Oct 7 10:37 study_before_workshop.html\n-rw-r--r-- 1 runner docker 4.7K Oct 7 10:34 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Oct 7 10:34 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:34 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:37 workshop.rmarkdown\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n\n\nhead 1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nhead -20 data/1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nSOURCE 3 ORGANISM_COMMON: SPERM WHALE; \nSOURCE 4 ORGANISM_TAXID: 9755; \nSOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \nSOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; \nSOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \nSOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15A \nKEYWDS HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS 2 TRANSPORT COMPLEX \nEXPDTA NEUTRON DIFFRACTION \nAUTHOR F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir" + "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like > on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.html\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.qmd\nworkshop.rmarkdown\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 136\ndrwxr-xr-x 2 runner docker 4096 Oct 7 10:56 data\ndrwxr-xr-x 2 runner docker 4096 Oct 7 10:56 images\n-rw-r--r-- 1 runner docker 1597 Oct 7 10:56 overview.qmd\n-rw-r--r-- 1 runner docker 184 Oct 7 10:56 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69876 Oct 7 10:58 study_before_workshop.html\n-rw-r--r-- 1 runner docker 4807 Oct 7 10:56 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Oct 7 10:56 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 8550 Oct 7 10:56 workshop.qmd\n-rw-r--r-- 1 runner docker 8564 Oct 7 10:58 workshop.rmarkdown\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 136K\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 images\n-rw-r--r-- 1 runner docker 1.6K Oct 7 10:56 overview.qmd\n-rw-r--r-- 1 runner docker 184 Oct 7 10:56 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69K Oct 7 10:58 study_before_workshop.html\n-rw-r--r-- 1 runner docker 4.7K Oct 7 10:56 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Oct 7 10:56 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:56 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:58 workshop.rmarkdown\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 144K\ndrwxr-xr-x 4 runner docker 4.0K Oct 7 10:58 .\ndrwxr-xr-x 5 runner docker 4.0K Oct 7 10:58 ..\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 7 10:56 images\n-rw-r--r-- 1 runner docker 1.6K Oct 7 10:56 overview.qmd\n-rw-r--r-- 1 runner docker 184 Oct 7 10:56 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69K Oct 7 10:58 study_before_workshop.html\n-rw-r--r-- 1 runner docker 4.7K Oct 7 10:56 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Oct 7 10:56 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:56 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 7 10:58 workshop.rmarkdown\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n\n\nhead 1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nhead -20 data/1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nSOURCE 3 ORGANISM_COMMON: SPERM WHALE; \nSOURCE 4 ORGANISM_TAXID: 9755; \nSOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \nSOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; \nSOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \nSOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15A \nKEYWDS HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS 2 TRANSPORT COMPLEX \nEXPDTA NEUTRON DIFFRACTION \nAUTHOR F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir" }, { "objectID": "core/week-2/workshop.html#differences-between-r-and-python",