namespace:doc-mach:preparation-course-bioinfo2020 [WIKI CEMCC]

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====== Review after the course ======

**MK20200117**

   * **Misunderstanding of technical term**
      * Metagenome != microbiome analysis by targeted amplicon sequencing (amplicon analysis of rRNA gene; meta16S/18S; community analysis)
      * Metagenome = ‘meta’ + ‘genome’; Genome = ‘gen’ + ‘ome’
      * Amplicon of rRNA gene = part of single gene, not genome!
      * Amplicon of rRNA gene of environment = ‘meta’ + rRNA gene, not 'meta' + 'genome'
  * **We need to improve basic knowledge of students about molecular biology and gene analysis (before genome analysis).**
      * Course of basics of gene and genome
      * Course of basics of web tools
  * It is appropriate to held the same couse "Introduction to Microbial Genomic and Metagenomic Analyses" annually, to update knowledge of genomics and metagenomics
      * This type of comprehensive course is more desirable than more specfic course of microbiome analysis, which is directly-related to their own research.
        * During this course for genomics/metagenomics, participants may have learned from more global aspects, and still they can apply what they learned to their amplicon studies.
      * In depth course might be held in future (but maybe such situation will not happen soon…)
        * Course of "Microbial Genomic Analyses" (note that without "Introduction of")
        * Course of "Metagenomic Analyses" (note that without "Introduction of")
  * Lecture organization was appropriate
      * Introduction of real studies (SF and MK)
        * We may emphasize clarification of microbiome amplicon studies and genomic/metagenomic studies more clearly
      * Introduction of algorithm
      * Practices of basics (MK and GL)
      * Introduction of statistics (GL)
      * Introduction of R
      * Lecture of knowledge of pangenome and related issues (MA)
      * Introduction of tools with graphics (MA)
  * Lecture based on real reasearch about statistical analysis will contribute to improvement of the effect of the course
      * Such as the ones provided at the beginning course by SF and MK and the one provided by MA
  * We may update contents of the course (MK, GL)
  * To avoid situation that participants (who are not motivated enough) get bored and leave the course mid-way, we may improve the contents by either of the following ways.
      * State at the beginning that they are better to attend through the end.
      * Improve practice of basics of linux to keep their motivation, whereas more concise introduction of command line.

====== Note ======

**To prepare**

  * <del>No call for participants!?</del>
  * Can we fix the number of participants? max 30, because of the number of notebook at cmcc practice room.
  * Can we select simply those 15 who applies first?
  * Those with some motivation letter or sentence attached will be regarded primarily.
  * bowtie
  * tutorial data download
  * wifi at the room?

**What computer will we use?**

  * Linux server, soroban
  * How accounts are created
  * How accounts info are distributed to participants

  * For R tutorial (3rd day), use CMCC 1st floor room, with 30 notebook, where Andrés has installed Rstudio on 2019/07.

**Questions MK200103**

  * When network becomes down, what will we do alternative

**Necessity of total hours**

  * 64hr = 8 days x 8hr
  * Instead of 8 days, we will do 9 days, with the first and the last day of half days (i.e. 4hr), and 7-days for 8hr.
  * Lab work e.g. 5hr

**Time course of 1 day**

  * Morning: 9:00-13:00, 4hr
  * Afternoon: 14:30-18:30, 4hr
  * In total, 8hr / day
  * 1h45min-30min break-1h45min / 4hr

**Room reservation**

  * depend on the number of participants
  * Windows computer at CMCC computer room

**About document**

  * Share documents, MK to Giovanni,

====== Program / Programación ======

===== Day 1. =====

<font 20px/Verdana, sans-serif;;#000000;;yellow>Day 1. Monday 6</font>  <font inherit/inherit;;inherit;;rgb(255, 255, 0)>14:30-18:30 (4hr)</font>

<font inherit/Verdana, sans-serif;;#000000;;yellow>KAWAI, FUJIYOSHI</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 1-1. (60-min) MK</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Opening remarks</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Outline of this course</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Brief review of introduction to Genomic, Metagenomic and Transcriptomic Anal</font>yses <font inherit/inherit;;inherit;;#f1c40f>M</font><font inherit/inherit;;inherit;;#f1c40f>K</font>*

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 1-2. (60-min) SF</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Microbial community analysis (Amplicon analysis, Metagenomics)</font><font inherit/inherit;;inherit;;#f1c40f>SF</font>*

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 2. (120-min) MK</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Statistical mind to find more concrete association with phenomena</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>What is your question / How to test your question / Importance of experimental design</font>

===== Day 2. =====

<font 20px/Verdana, sans-serif;;#000000;;#ffff00>Day 2. Tuesday 7 9:00</font>  <font inherit/inherit;;inherit;;yellow>ÁVILA</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 3. (120-min) AA</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Sequencers, sequencing platform (Illumina, long read)</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Basic data format of basic sequence data (FASTA, GENBANK)</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Basic data format of 'next-generation' sequence (NGS) data (FASTQ)</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Quality information of positions of reads</font>

<font medium/Verdana, sans-serif;;#000000;;#33ccff>Lab session 1. (120-min)</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 4. 14:30 (120-min) AA</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Sequence alignment, sequence similarity search</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Two basic approaches, mapping and assembly</font>

<font medium/Verdana, sans-serif;;#000000;;#33ccff>Lab session 2. (120-min)</font>

===== Day 3. =====

<font 20px/Verdana, sans-serif;;#000000;;yellow>Day 3. Wednesday 8 9:00 KAWAI,</font>  <font 20px/inherit;;inherit;;#ffff00>LARAMA</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Practice 1. (120-min) GL</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>UNIX basic command, to sniff around sequence files (cd, pwd, ls etc.)</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Examine file contents of MiSeq</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>File organization, concept of Path</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Practice 2. (120-min) GL</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Text processing (grep, less, tail, head,..)</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>To get familiar with NGS sequences #1 (examine NGS sequence files)</font>
  * <font 14.666666984558105px/inherit;;inherit;;inherit>Check contents of fastq</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Practice 3. (120-min) MK</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Text processing (wc, cut, sed, awk, redirect (> , >> ) etc.), gzip</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>To get familiar with NGS sequences #2 (sequential commands by pipe)</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>count how many of reads of fastq</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Practice 4. (120-min) MK</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Shell script (Batch processing)</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Editor (vim)</font>

===== Day 4. =====

<font 20px/Verdana, sans-serif;;#000000;;yellow>Day 4. Thursday 9 9:00 KAWAI,</font>  <font 20px/Verdana, sans-serif;;#000000;;#ffff00>LARAMA</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Practice 6. (120-min) GL</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>R statistics and graphics language #1</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Practice 7. (120-min) GL</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>R statistics and graphics language #2</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Goal:</font> * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Do (small) analysis and make report of statistical test (apa format)</font>

<font medium/Verdana, sans-serif;;#000000;;#33ccff>Lab session 3. (240-min)</font>

===== Day 5. =====

<font 20px/Verdana, sans-serif;;#000000;;yellow>Day 5. Friday 10 9:00 KAWAI,</font>  <font 20px/inherit;;inherit;;#ffff00>LARAMA</font><font inherit/inherit;;inherit;;yellow>, ÁVILA</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 6. (120-min) GL</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Quality control of raw sequence data, basic tools for sequence and NGS data</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Commands for NGS analyses</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Commands for sequence analyses</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Brief review of online resources / web services</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>NGSToolkit (instead of FastQC)</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Practice 8. (120-min) MK</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>To get familiar with NGS sequences #3</font>
  * <font inherit/Verdana, sans-serif;;inherit;;inherit>make your own pipeline for custom analysis and record of analysis</font>* <font inherit/Verdana, sans-serif;;inherit;;inherit>screen command</font>* <font 11pt/Verdana, sans-serif;;inherit;;inherit>Sequence similarity search against a genome at hand (Do BLAST search locally)</font>

<font 16px/Verdana, sans-serif;;inherit;;#33ccff>Lab XX (240-min)</font>

===== Day 6. =====

<font 20px/Verdana, sans-serif;;#000000;;yellow>Day 6. Monday 13 9:00 ÁVILA</font>   , (<font inherit/inherit;;inherit;;#ffff00>LARAMA</font>)

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 7 and Practice 9. (240-min)</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Public sequence database</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Local mirror of databases</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Usage of information of public database</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>e.g. Mapping (bowtie2)</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 8 and Practice 10. (240-min)</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Genome assembly</font>

===== Day 7. =====

<font 20px/Verdana, sans-serif;;#000000;;yellow>Day 7. Tuesday 14 9:00 KAWAI</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 9 and Practice 11. (120-min) MK</font>

 \\
* <font 11pt/Verdana, sans-serif;;inherit;;inherit>Protein-coding gene prediction, RNA-coding gene prediction, gene annotation → MK</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Muliple sequence alignment</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>protein domain search</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 10 and Practice 12. (120-min) MK</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Gene contents of genome</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Concept of ortholog</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Concept of conserved single-copy genes</font>

<font medium/Verdana, sans-serif;;#000000;;#33ccff>Lab session 2. (240-min)</font>

===== Day 8. =====

<font 20px/Verdana, sans-serif;;#000000;;yellow>Day 8. Wednsday 15</font>  <font inherit/inherit;;inherit;;#ffcc33>9:00 - 13:00</font><font inherit/inherit;;inherit;;yellow>ABANTO</font>

<font medium/Verdana, sans-serif;;#000000;;#00ff66>Lecture 10 and Practice 12. (240-min)</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Introduction of analyses</font>

  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Pangenome</font>
  * <font 11pt/Verdana, sans-serif;;inherit;;inherit>Phylogenetic tree</font>

<font medium/Verdana, sans-serif;;#000000;;#33ccff>Lab session 2. (240-min)</font>

===== Day 9. =====

<font 20px/Verdana, sans-serif;;#000000;;#ffff00>Day 9. Thursday 16 9:00 KAWAI, LARAMA</font>

<font medium/Verdana, sans-serif;;#000000;;#33ccff>Lab session 2. (240-min)</font>

  * Discuss plans
  * groups work
  * proposal
  * paper introducce
  * apply what they learned

<font medium/Verdana, sans-serif;;#000000;;#33ccff>Internal meeting (120-min)</font>