Difference between revisions of "Sounkou Kim"
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| − | < | + | <p><b><span style="font-size: x-large">Principles of Bioinformatics</span></b></p> |
| − | < | + | <h2><b><span style="font-size: large">Bioprogramming</span></b></h2> |
| − | <p> Threre are some example that use the word 'Bio Programming' as a technique in genetic engineering related to synthetic biology such as synthesizing or modifying biological object like DNA, proteins, or even cells. <a href="http://www.technologyreview.com/article/404707/bio-programming/">[1]</a><a href="http://aihub.net/bio-programming-hacking-dna-compiling-code-living-systems/">[2]</a> Therefore, to avoid confusion, the word 'Bioprogramming' written without blank would be limitted in meaning as programming in computer used to bioinformatics in 2015 1st semestser Bioinformatics class.</p> | + | <p> Threre are some example that use the word 'Bio Programming' as a technique in genetic engineering related to synthetic biology such as synthesizing or modifying biological object like DNA, proteins, or even cells. <a href="http://www.technologyreview.com/article/404707/bio-programming/">[1]</a><a href="http://aihub.net/bio-programming-hacking-dna-compiling-code-living-systems/">[2]</a> Therefore, to avoid confusion, the word 'Bioprogramming' written without blank would be limitted in meaning as programming in computer used to bioinformatics in 2015 1st semestser Bioinformatics class. Professor Bhak suggested following two examples:</p> |
| − | < | + | <ul> |
| − | < | + | <li><a href="http://www.biophp.org/">BioPHP</a></li> |
| − | < | + | </ul> |
| − | < | + | <p style="margin-left: 40px">BioPHP is a package of PHP, with classes for DNA and protein sequence analysis, alignment, database parsing, and othe bioinformatics tools. It is not independent programming language from PHP, but a bunch of add-on tools specialized in bioinformatics. <a href="http://en.wikipedia.org/wiki/BioPHP">http://en.wikipedia.org/wiki/BioPHP</a></p> |
| − | < | + | <ul> |
| + | <li><a href="http://www.bioperl.org/wiki/Main_Page">BioPerl</a></li> | ||
| + | </ul> | ||
| + | <p style="margin-left: 40px">BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. <a href="http://en.wikipedia.org/wiki/BioPerl">http://en.wikipedia.org/wiki/BioPerl</a> </p> | ||
| + | <p> As shown in both examples, bioprogramming does not mean by the original programming language only for bioinformatics, but the use of existing general programming language such as Java<a href="http://www.ijcse.com/docs/INDJCSE11-02-06-087.pdf">[3]</a> or R<a href="http://cran.r-project.org/doc/contrib/Krijnen-IntroBioInfStatistics.pdf">[4]</a> specially for bioinformatics. There is even bioinformatics-specialized OS, <a href="http://environmentalomics.org/bio-linux/">Bio-Linux</a>, the Linux distribution with pakages of bioinformatics tools in OS level.</p> | ||
| + | <h2>Genomics</h2> | ||
| + | <p> Genomics is a study on sequencing, analysing, or modifying genome, the complete set of DNA within an organism. Based on development in sequencing technology and followed completion of genome sequencing, the "omics" reolution - the study on 'total' thing about the subject - had begun. By dealing with functions of gene, structures of translated protein, modifying and recovering genes, genomics can be applied in development of genomic medicine or synthetic biology.</p> | ||
| + | <h2>Transcriptomics</h2> | ||
| + | <p> Transcriptome is the set of all transcripted materials, such as mRNA, rRNA, tRNA and other non-coding RNA. Just like genomics study all about genome, transcriptomics study all about transcriptome. Old <a href="http://en.wikipedia.org/wiki/DNA_microarray">DNA microarray</a> and new <a href="http://en.wikipedia.org/wiki/RNA-Seq">RNA-Seq</a> are mainly used technologies for transcriptomics. Along the flow of genomic information transfer, transcriptomics can refer genomics or can be referred by proteomics.</p> | ||
| + | <ul> | ||
| + | <li>RNA-Seq</li> | ||
| + | </ul> | ||
| + | <p style="margin-left: 40px;">Also called Whole Transcriptome Shotgun Sequencing (WTSS). To reveal a snapshot of RNA presence and quantity from a genome for given time interval, uses <a href="http://en.wikipedia.org/wiki/DNA_sequencing#Next-generation_methods">next-generation sequencing</a> thechnology. Analyses gene expression, single nucleotide variation discovery, post-transcriptional single nucleotide variants, fusion gene detection, or coexpression network. Enables study of transcriptomics for providing or modifying the sample.</p> | ||
| + | <h2>Proteomics</h2> | ||
| + | <p><a href="http://fold.it/portal/">http://fold.it/portal/</a></p> | ||
| + | <p><a href="http://www.nature.com/nbt/journal/v30/n2/full/nbt.2109.html">http://www.nature.com/nbt/journal/v30/n2/full/nbt.2109.html</a></p> | ||
| + | <p><a href="https://www.youtube.com/watch?v=bo99JjnfdA8">https://www.youtube.com/watch?v=bo99JjnfdA8</a></p> | ||
| + | <h2>Epigenomics and Phenomics</h2> | ||
| + | <h2>Canceromics and Geromics</h2> | ||
<p> </p> | <p> </p> | ||
Latest revision as of 07:47, 29 May 2015
Principles of Bioinformatics
Contents
Bioprogramming
Threre are some example that use the word 'Bio Programming' as a technique in genetic engineering related to synthetic biology such as synthesizing or modifying biological object like DNA, proteins, or even cells. [1][2] Therefore, to avoid confusion, the word 'Bioprogramming' written without blank would be limitted in meaning as programming in computer used to bioinformatics in 2015 1st semestser Bioinformatics class. Professor Bhak suggested following two examples:
BioPHP is a package of PHP, with classes for DNA and protein sequence analysis, alignment, database parsing, and othe bioinformatics tools. It is not independent programming language from PHP, but a bunch of add-on tools specialized in bioinformatics. http://en.wikipedia.org/wiki/BioPHP
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. http://en.wikipedia.org/wiki/BioPerl
As shown in both examples, bioprogramming does not mean by the original programming language only for bioinformatics, but the use of existing general programming language such as Java[3] or R[4] specially for bioinformatics. There is even bioinformatics-specialized OS, Bio-Linux, the Linux distribution with pakages of bioinformatics tools in OS level.
Genomics
Genomics is a study on sequencing, analysing, or modifying genome, the complete set of DNA within an organism. Based on development in sequencing technology and followed completion of genome sequencing, the "omics" reolution - the study on 'total' thing about the subject - had begun. By dealing with functions of gene, structures of translated protein, modifying and recovering genes, genomics can be applied in development of genomic medicine or synthetic biology.
Transcriptomics
Transcriptome is the set of all transcripted materials, such as mRNA, rRNA, tRNA and other non-coding RNA. Just like genomics study all about genome, transcriptomics study all about transcriptome. Old DNA microarray and new RNA-Seq are mainly used technologies for transcriptomics. Along the flow of genomic information transfer, transcriptomics can refer genomics or can be referred by proteomics.
- RNA-Seq
Also called Whole Transcriptome Shotgun Sequencing (WTSS). To reveal a snapshot of RNA presence and quantity from a genome for given time interval, uses next-generation sequencing thechnology. Analyses gene expression, single nucleotide variation discovery, post-transcriptional single nucleotide variants, fusion gene detection, or coexpression network. Enables study of transcriptomics for providing or modifying the sample.
Proteomics
http://www.nature.com/nbt/journal/v30/n2/full/nbt.2109.html
https://www.youtube.com/watch?v=bo99JjnfdA8
Epigenomics and Phenomics
Canceromics and Geromics
