diff --git a/assets/images/genomics_intro.jpg b/assets/images/genomics_intro.jpg new file mode 100644 index 00000000000000..009469def53d6e Binary files /dev/null and b/assets/images/genomics_intro.jpg differ diff --git a/assets/images/genomics_intro.png b/assets/images/genomics_intro.png new file mode 100644 index 00000000000000..c854ceb8eb7656 Binary files /dev/null and b/assets/images/genomics_intro.png differ diff --git a/learning-pathways/data-driven-biology.md b/learning-pathways/data-driven-biology.md new file mode 100644 index 00000000000000..b529080295b671 --- /dev/null +++ b/learning-pathways/data-driven-biology.md @@ -0,0 +1,23 @@ +--- +layout: learning-pathway +cover-image: /assets/images/genomics_intro.png +cover-image-alt: "Genomics intro" +tags: [introduction, real-course] +editorial_board: +- nekrut + +draft: true + +title: Introduction to Data Driven Life Sciences +description: | + This learning path starts with the history of biology and takes you on a journey through fundamental data analysis techniques and their applications. + +pathway: + - section: "Module 1: History" + description: Knowing history is essential for understanding how we arrived to the current state of affairs in our field + tutorials: + - name: gnmx-lecture1 + topic: data-science + + +--- diff --git a/topics/data-science/metadata.yaml b/topics/data-science/metadata.yaml index 8daf2b876c7bbe..018069f9818aa6 100644 --- a/topics/data-science/metadata.yaml +++ b/topics/data-science/metadata.yaml @@ -27,7 +27,9 @@ subtopics: - id: sciwms title: "Scientific Workflow Management Systems" description: "Here you can find brief tutorials on a couple different workflow engines that you might encounter in the wild." - + - id: gnmx + title: "Introduction to Genomics" + description: "A data- and galaxy-driven introduction to genomics" editorial_board: - hexylena - shiltemann diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/berg.png b/topics/data-science/tutorials/gnmx-lecture1/images/berg.png new file mode 100644 index 00000000000000..8bfd0aab394c60 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/berg.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/blender.png b/topics/data-science/tutorials/gnmx-lecture1/images/blender.png new file mode 100644 index 00000000000000..15c9fd462be4ed Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/blender.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/books.png b/topics/data-science/tutorials/gnmx-lecture1/images/books.png new file mode 100644 index 00000000000000..f5ba20db3ca86c Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/books.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/cfww.png b/topics/data-science/tutorials/gnmx-lecture1/images/cfww.png new file mode 100644 index 00000000000000..2ab87936359f76 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/cfww.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/darwin.png b/topics/data-science/tutorials/gnmx-lecture1/images/darwin.png new file mode 100644 index 00000000000000..f81d1b6b3f4c36 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/darwin.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/darwin_nature.png b/topics/data-science/tutorials/gnmx-lecture1/images/darwin_nature.png new file mode 100644 index 00000000000000..ed05416aa09093 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/darwin_nature.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/dct.png b/topics/data-science/tutorials/gnmx-lecture1/images/dct.png new file mode 100644 index 00000000000000..d80acde3856701 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/dct.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/dlh.png b/topics/data-science/tutorials/gnmx-lecture1/images/dlh.png new file mode 100644 index 00000000000000..7e745e2cd38a78 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/dlh.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/ljm.png b/topics/data-science/tutorials/gnmx-lecture1/images/ljm.png new file mode 100644 index 00000000000000..d62e84c8fa6cd0 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/ljm.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/lt.png b/topics/data-science/tutorials/gnmx-lecture1/images/lt.png new file mode 100644 index 00000000000000..302746eb01fdd1 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/lt.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/luria_small.png b/topics/data-science/tutorials/gnmx-lecture1/images/luria_small.png new file mode 100644 index 00000000000000..2c4d183e3cd130 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/luria_small.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/mendel_cartoon.png b/topics/data-science/tutorials/gnmx-lecture1/images/mendel_cartoon.png new file mode 100644 index 00000000000000..be04bab18b0a8f Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/mendel_cartoon.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/mendel_reexamination.png b/topics/data-science/tutorials/gnmx-lecture1/images/mendel_reexamination.png new file mode 100644 index 00000000000000..0b94eb6a89535f Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/mendel_reexamination.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/mendel_results.png b/topics/data-science/tutorials/gnmx-lecture1/images/mendel_results.png new file mode 100644 index 00000000000000..d45a925ad06cbd Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/mendel_results.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/ms.png b/topics/data-science/tutorials/gnmx-lecture1/images/ms.png new file mode 100644 index 00000000000000..aa2dc644fcf1f8 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/ms.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/ms1.png b/topics/data-science/tutorials/gnmx-lecture1/images/ms1.png new file mode 100644 index 00000000000000..8bc8107931f26d Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/ms1.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/ms2.png b/topics/data-science/tutorials/gnmx-lecture1/images/ms2.png new file mode 100644 index 00000000000000..7bdcf4d4e1c305 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/ms2.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/muller_scribble.png b/topics/data-science/tutorials/gnmx-lecture1/images/muller_scribble.png new file mode 100644 index 00000000000000..ef8bee4a938171 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/muller_scribble.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/pcr1.png b/topics/data-science/tutorials/gnmx-lecture1/images/pcr1.png new file mode 100644 index 00000000000000..aad013535a95f3 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/pcr1.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/pcr2.png b/topics/data-science/tutorials/gnmx-lecture1/images/pcr2.png new file mode 100644 index 00000000000000..5241be7626cae4 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/pcr2.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/reg.png b/topics/data-science/tutorials/gnmx-lecture1/images/reg.png new file mode 100644 index 00000000000000..01c0e43a3acc07 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/reg.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/three_papers.png b/topics/data-science/tutorials/gnmx-lecture1/images/three_papers.png new file mode 100644 index 00000000000000..e9a39a6d7146ad Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/three_papers.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/images/wsgm.png b/topics/data-science/tutorials/gnmx-lecture1/images/wsgm.png new file mode 100644 index 00000000000000..bc2dd76625a442 Binary files /dev/null and b/topics/data-science/tutorials/gnmx-lecture1/images/wsgm.png differ diff --git a/topics/data-science/tutorials/gnmx-lecture1/slides.html b/topics/data-science/tutorials/gnmx-lecture1/slides.html new file mode 100644 index 00000000000000..f233fc4897044a --- /dev/null +++ b/topics/data-science/tutorials/gnmx-lecture1/slides.html @@ -0,0 +1,281 @@ +--- +layout: tutorial_slides +logo: assets/images/genomics_intro.png +title: "A brief history of modern biology" +video: false +contributions: + authorship: + - nekrut +--- + +# Charles Darwin +.center[The fabric of biology: 1809 - 1882] + +![Darwin](./images/darwin.png) + +Provisional theory of pangenesis. All sperm, egg, buds consisted of multitude of gemmules given off by “ *each separate atom of the organism* ”. + +--- + +# Francis Galton +.center[Experimental validation: 1822 - 1911] + +![Galton](https://upload.wikimedia.org/wikipedia/commons/thumb/6/6e/Sir_Francis_Galton_by_Gustav_Graef.jpg/453px-Sir_Francis_Galton_by_Gustav_Graef.jpg) + +Blood transfusion in rabbits produces no evidence to support provisional theory of pangenesis. + +--- + +# Darwin gets pissed + +![Darwin letter to Nature](./images/darwin_nature.png) + +--- + +# Gregor Johann Mendel + +.center[Quantifiable heredity: 1822 - 1884] + +.pull-left[ +![Mendel](https://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Gregor_Mendel_2.jpg/442px-Gregor_Mendel_2.jpg) +] + +.pull_right[ +- Born in Austro-Hungarian Empire (1822) +- Admitted at the Augustinian monastery in Brno (1843) +- Studies in Vienna with Doppler, Ettinghausen, Redtenbacher, Fenzl, and Unger (1851 - 1853) +- Teaches at the Monastery (1853 - 1868) +- Grows 28,000 plants and analyzed seven pairs of traits +] + +--- + +# Mendel gets lucky + +![Mendel results](./images/mendel_results.png) + +.footnote[(From [Magner 2002](https://isbnsearch.org/isbn/0824708245))] + +--- + +![Mendel cartoon](./images/mendel_cartoon.png) + +.footnote[(From [Gonick Wheelis 1991](https://isbnsearch.org/isbn/9780062730992))] + +--- + +# Perhaps too lucky + +![Mendel re-examination](./images/mendel_reexamination.png) + +.footnote[(From [Sturtevant 2001](https://isbnsearch.org/isbn/9780879696078))] + +--- + +# deVreis/Correns/Tschemak + +.center[The Rediscovery] + +![DCT](./images/dct.png) + +--- + +# Meanwhile chromosomal theory evolves + +.center[ + +- Species have a constant number of chromosomes +- Equal numbers come from egg and sperm +- Reduction is accomplished by divisions +- Chromosomes are bearers of hereditary material + +] + +--- + +# The fly room + +.center[ + +Morgan/Sturtevant/Bridges/Muller + +- Chromosomes contain hereditary information +- Genes are linearly distributed along chromosome +- Gene is a unit of information +- Gene can define characteristics such as eye color, wing shape etc. + +] + +--- + +# Academic competition! + +![Muller Scribble](./images/muller_scribble.png) + +.footnote[(From [Carson 2004](https://www.amazon.com/Elof-Axel-Carlson-Classical-2004-03-13/dp/B00DJ4VBXY))] + +--- + +# But what is the carrier of information? + +- **Miescher** | nucleic acids +- **Kossel** | DNA, RNA, histones +- **Levene** | tetranucleotide theory +- **Chargaff** | parity rules +- **Griffith, Avery, MacLeod, McCarty** | nucleic acid is the transforming factor + +--- + +# The Church of Phage + +- **Delbrück, Luria, Hershey** | replication and genetic structure of viruses +- **Lwoff** | profage and lysogeny +- **Lederberg, Hayes** | bacterial sex, plasmids +- **Hershey, Chase** | DNA = heredity +- **Watson** | ... + +--- + +# Delbrück, Luria, Hershey + +![dlh](./images/dlh.png) + +NP 1969: " *discoveries concerning the replication mechanism and genetic structure of viruses* " + +--- + +# Luria Delbrück Experiment + +![Fluctuation test](https://upload.wikimedia.org/wikipedia/commons/thumb/d/d3/Luria-delbruck_diagram.svg/459px-Luria-delbruck_diagram.svg.png) + +--- + +# Hershey-Chase experiment + +.pull-left[ +![Hershey and Chase](https://upload.wikimedia.org/wikipedia/commons/thumb/b/b3/Scientist_Alfred_Hershey_and_Martha_Chase.jpg/754px-Scientist_Alfred_Hershey_and_Martha_Chase.jpg) +] + +.pull-right[ +![Hershey-Chase experiment](https://upload.wikimedia.org/wikipedia/commons/thumb/3/32/Hershey_Chase_experiment.png/758px-Hershey_Chase_experiment.png) +] + +--- + +# Lederberg-Tatum experiment + +Genetic recombination in *E. coli* + +![Lederberg-Tatum Experiment](./images/lt.png) + +--- + +# Blender again! + +![Genetic distance in bacteria](./images/blender.png) + +--- + +# DNA + +- **Crick, Franklin, Watson, Wilkins** | the structure of DNA +- **Meselson, Stahl** | semiconservative replication +- **Ochoa, Kornberg** | enzymatic synthesis of nucleic acids +- **Holley, Nirenberg, Khorana** | the code + +--- + +# Crick, Franklin, Watson, Wilkins + +DNA is an antiparallel double helix + +![Crick, Franklin, Watson, Wilkins](./images/cfww.png) + +--- + +![Three papers](./images/three_papers.png) + +--- + +# Meselson, Stahl + +DNA replication is semiconservative + +![Meselson, Stahl](./images/ms.png) + +--- + +# Meselson-Stahl experiment + +CsCl gradient centrifugation + +![Meselson, Stahl experiment 1](./images/ms1.png) + +--- + +![Meselson, Stahl experiment 2](./images/ms2.png) + +--- + +# Gene function + +- **Lwoff, Jacob, Monod** | genetic map and gene regulation +- **Beadle, Tatum** | one gene = one protein +- **Pauling, Ingram** | molecular disease + +--- + +# Lwoff, Jacob, Monod + +Lysogeny, prophage, genetic maps, gene regulation + +![Lwoff, Jacob, Monod](./images/ljm.png) + +--- + +![Regulation](./images/reg.png) + +--- + +# Reverse Transcription, Recombinant Age + +- **Temin, Baltimore** | reverse transcription +- **Cohen, Boyer** | recombinant methodologies +- **Berg** | SV40 +- **Maxam, Gilbert, Sanger** | sequencing is here + +--- + +# Berg experiment + +![Berg experiment](./images/berg.png) + +--- + +# PCR + +.pull-left[ +![PCR1](./images/pcr1.png) +] + +.pull-right[ +![PCR2](./images/pcr2.png) +] + +--- + +# DNA Sequencing is here! + +![Wu, Sanger, Gilbert, Mullis](./images/wsgm.png) + + + + + + + + + + + + diff --git a/topics/data-science/tutorials/gnmx-lecture1/tutorial.md b/topics/data-science/tutorials/gnmx-lecture1/tutorial.md new file mode 100644 index 00000000000000..7787fdef9496f7 --- /dev/null +++ b/topics/data-science/tutorials/gnmx-lecture1/tutorial.md @@ -0,0 +1,51 @@ +--- +layout: tutorial_hands_on + +title: "A (very) brief history of genomics" +questions: + - What is this course about? + - What is the history of genomics? +objectives: + - Have a basic understanding of history of biology from Darwin to today. +time_estimation: "1h" +key_points: + - Jim Watson did not discover DNA +contributions: + authorship: + - nekrut + +subtopic: gnmx +draft: true +--- + +![Fluctuation test](./images/luria_small.png) + +# What do you know? + +This is the first lecture of the class. We will begin with a short quiz that is designed tio let me know what you do and do not know. This quiz will have no effect on your grade in this course. + +# Why history? + +Knowing history is essential for understanding how we arrived to the current state of affairs in our field. It is also full of accidental discoveries and dramatic relationships making it quite interesting to read about. I strongly advise you to take a look at the manuscripts below: + +## Classical publications + +* 1965 : [A history of genetics](http://www.amazon.com/A-History-Genetics-A-H-Sturtevant/dp/0879696079) +* 1943 : [Delbruck & Luria](http://www.bx.psu.edu/~anton/bioinf1-2014/delbruck-luria-1943.pdf) +* 1944 : [Avery, MacLeod, & McCarty](http://www.bx.psu.edu/~anton/bioinf1-2014/avery-1944.pdf) +* 1952 : [Herhey & Chase](http://www.bx.psu.edu/~anton/bioinf1-2014/hershey-chase-1952.pdf) +* 1953 : [Watson & Crick](http://www.bx.psu.edu/~anton/bioinf1-2014/watsoncrick.pdf) +* 1958 : [Meselson & Stahl](http://www.bx.psu.edu/~anton/bioinf1-2014/Proc%20Natl%20Acad%20Sci%20USA%201958%20Meselson.pdf) +* 1960 : [Jacob and Monod](http://www.bx.psu.edu/~anton/bioinf1-2014/jacob-monod-1961.pdf) + +## Popular (yet very informative) literature + +![Books](./images/books.png) + +------ + +# Let's get to it + +Today's lecture will be organized as a, well, a lecture - we will be going over a set of slides linked at the beginning of this page. + +-----