Transcript: Subject 3 biological mean three Conclusion what does it mean? two Subject 2 computational mean is here Subject 3 And one more thing... Thank you for your attention!
Transcript: Introduction History About Bioinformatics Species Used: Sylvilagus audubonii (Desert Cottontail) Sylvilagus aquaticus (Swamp Rabbit) Sylvilagus palustris (Marsh Rabbit) Sylvilagus floridanus (Eastern Cottontail) Sylvilagus nuttallii (Mountain Cottontail) Outgroup: Brachylagus idahoensis (Pygmy Rabbit) Discussion Analysis of Genetic Distances Paulien Hogeweg and Ben Hesper Fredrick Sager Margaret Oakley Dayhoff Species Used Different areas of cytochrome b Part 1 DNA (nucleotide) sequences retrieved from NCBI website and then aligned Accession codes recorded Part 2 "Neighbor Joining: Phenetic Tree" created and condensed through the MEGA5 program, according to protocol "Maximum Parsimony: Cladistic Tree" created and condensed through the MEGA5 program, according to protocol Genetic distances between pairs of taxa computed and recorded Works Cited Why Were the Bootstrap Values So Low? Molly McElvogue and Megan Turner Exploring Evolutionary Relationships between Species: A Comparison of Sequences of Cytochrome B Results Bioinformatics Bioinformatics and Genetics Nydam, M. and Wooten, J. 2014. Bioinformatics Protocol, BIO 210 Lab Handout. http://en.wikipedia.org/wiki/Rabbit http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068925/ http://bioinformaticsweb.net/his.html Discussion audubonii and palustris smallest distance (most similar) of .029 aquaticus and audubonii distance of .093 All other distances relatively equal From .110-.180 Largest distance, most dissimilar, idahoensis and nuttallii at .182 opposite of hypothesis floridanus and palustris only .110 Regarding the Evolutionary Relationships of the Selected Species Analysis of Phylogenetic Trees MS2 and PhiX174 Modern Applications and its Use in this Experiment Upon research of each species, it was hypothesized that while, all species would be closely related, being, besides the pygmy, members of the genera Sylivilagus, the cottontails: the mountain cottontail, the desert cottontail, and the pygmy rabbit (outgroup) would be very genetically similar to each other (based on geography) the swamp rabbit, eastern cottontail, and marsh rabbit would be very genetically similar to each other (based on geography) the eastern cottontail and marsh rabbit would be the most genetically similar overall (based on morphological traits) Results Genetic Distances Important People Rabbits: Genus Sylvilagus Methods Neighbor Joining: Phenetic Tree Maximum Parsimony: Cladistic Tree Results Possible Error Hypothesis Definition: a field of study that develops different methods and technology in order to understand biological data, ultimately combining computer science, statistics, mathematics, and engineering Neighbor Joining: Phenetic Tree Bootstrap value of 100 for node of Sylvilagus audubonii and Sylvilagus palustris Bootstrap value of 65 for node of Sylvilagus aquaticus and the species listed above Maximum Parsimony: Cladistic Tree Bootstrap value of 98 for node of Sylvilagus audubonii and Sylvilagus palustris Neither Conclusive Phenetic Tree slightly more detailed
Transcript: Example of a Jeopardy Template By: Laken Feeser and Rachel Chapman When creating without a template... http://www.edtechnetwork.com/powerpoint.html https://www.thebalance.com/free-family-feud-powerpoint-templates-1358184 Example of a Deal or No Deal Template PowerPoint Game Templates There are free templates for games such as jeopardy, wheel of fortune, and cash cab that can be downloaded online. However, some templates may cost more money depending on the complexity of the game. Classroom Games that Make Test Review and Memorization Fun! (n.d.). Retrieved February 17, 2017, from http://people.uncw.edu/ertzbergerj/msgames.htm Fisher, S. (n.d.). Customize a PowerPoint Game for Your Class with These Free Templates. Retrieved February 17, 2017, from https://www.thebalance.com/free-powerpoint-games-for-teachers-1358169 1. Users will begin with a lot of slides all with the same basic graphic design. 2. The, decide and create a series of questions that are to be asked during the game. 3. By hyper linking certain answers to different slides, the game jumps from slide to slide while playing the game. 4. This kind of setup is normally seen as a simple quiz show game. Example of a Wheel of Fortune Template https://www.teacherspayteachers.com/Product/Wheel-of-Riches-PowerPoint-Template-Plays-Just-Like-Wheel-of-Fortune-383606 Games can be made in order to make a fun and easy way to learn. Popular game templates include: Family Feud Millionaire Jeopardy and other quiz shows. http://www.free-power-point-templates.com/deal-powerpoint-template/ Quick video on template "Millionaire" PowerPoint Games Some games are easier to make compared to others If users are unsure whether or not downloading certain templates is safe, you can actually make your own game by just simply using PowerPoint. add logo here References Example of a Family Feud Template PowerPoint Games are a great way to introduce new concepts and ideas You can create a fun, competitive atmosphere with the use of different templates You can change and rearrange information to correlate with the topic or idea being discussed. Great with students, workers, family, etc. For example: With games like Jeopardy and Family Feud, players can pick practically any answers. The person who is running the game will have to have all of the answers in order to determine if players are correct or not. However, with a game like Who Wants to be a Millionaire, the players only have a choice between answers, A, B, C, or D. Therefore, when the player decides their answer, the person running the game clicks it, and the game will tell them whether they are right or wrong.
Transcript: Obstacle 3 Why is it used? Just kidding, bioinformatics is the application of computer technology to the managementof biological information. How is it used? The end!! TEAM: THONG Obstacle 1 What is bioinformatics Obstacle 2 Bioinformatics is used to find out how things work, and to solve biological problems USES: Waste clean up Alternative energy sources anti-biotic resistance vetinary science drug development and much more... I don't really know.. Lets scientists compile biological data, allowing researchers to store data in the form of databases. Protein sequence protein structure can be determined Future of technology rests on Bioinformatics Bioinformatics!!! By: javier, autavius, and MARQUIS! Bioinformsatics
Transcript: Computational genomics Etudes de maladies grave avec traitement long Modelling biological systems Computational biology Phylogenetics Any question? Outline Definition Different fields Hopes for our future Manon GOGUERY - GI05 Definition Different application fields Bioinformatics Interdisciplinary field that develops methods and software tools for understanding biological data Combines computer science, statistics, biology and engineering Its aim is to solve scientific problems posed by biology Hopes for the future
Transcript: What is bioinformatics? Anders Krogh, Michael Brown, I.Saira Mian, Kimmen Sjölander, David Haussler. "Hidden Markov Models in Computational Biology: Applications to Protein Modeling". 9th November. "Assembling a Flood." ASCR Discovery. N.p., Nov. 2015. Web. 12 Nov. 2015. <http://ascr-discovery.science.doe.gov/2015/11/assembling-a-flood/>. Bioinformatics. Northeastern University College of Science, n.d. Web. 12 Nov. 2015. <http://www.northeastern.edu/bioinformatics/>. Eisenstein, Michael. "Big Data: The Power of Petabytes." Michele R. Forman PhD, Sarah M. Greene MPH, Nancy E. Avis PhD, Stephen H. Taplin MD, Paul Courtney MS, Peter A. Schad PhD, Bradford W. Hesse PhD and Deborah M. Winn PhD. "Bioinformatics". 9th November. Mullin, Emily. "How Bioinformatics Could Find The Next Breakthrough Cancer Drug." Forbes. Forbes Magazine, 12 Aug. 2015. Web. 11 Nov. 2015. <http://www.forbes.com/sites/emilymullin/2015/08/12/how-bioinformatics-could-finding-the-next-breakthrough-cancer-drug/> Nature.com. Nature Publishing Group, 4 Nov. 2015. Web. 11 Nov. 2015. <http://www.nature.com/nature/journal/v527/n7576_supp/full/527S2a.html>. "Research - College of Science." College of Science. Northeastern University, n.d. Web. 12 Nov. 2015. <http://www.northeastern.edu/cos/experiential-learning-co-op/research/>. Skrabanek, Luce . "Bioinformatics History and Introduction ." Cornell University. Web. 13 Nov. 2015. <http://chagall.med.cornell.edu/BioinfoCourse/presentations2010/Lecture1_2010.pdf> Thampi, Sabu M. "BioInformatics." (n.d.): n. pag. Web. 13 Nov. 2015. <http://arxiv.org/ftp/arxiv/papers/0911/0911.4230.pdf>. Universitat Autonoma DeBarcelona. MCs in Bioinformatics. 2015. Web. 9th November. Sources QUESTION Will I gain work experience? Christopher Brown Vincent Carlino Luke Janik Mitko Nikolov How should I get started? Mullin, Emily. "How Bioinformatics Could Find The Next Breakthrough Cancer Drug." Forbes. Forbes Magazine, 12 Aug. 2015. Web. 11 Nov. 2015. <http://www.forbes.com/sites/emilymullin/2015/08/12/how-bioinformatics-could-finding-the-next-breakthrough-cancer-drug/> "Assembling a Flood." ASCR Discovery. N.p., Nov. 2015. Web. 12 Nov. 2015. <http://ascr-discovery.science.doe.gov/2015/11/assembling-a-flood/>. Eisenstein, Michael. "Big Data: The Power of Petabytes." Nature.com. Nature Publishing Group, 4 Nov. 2015. Web. 11 Nov. 2015. <http://www.nature.com/nature/journal/v527/n7576_supp/full/527S2a.html>. Faster Genome Sequencing - Analysis of function, expression and interaction of all genes in an organism - Analyzes the relationship between a person's genome and their phenotype What specifically Bioinformatics is Proteomics QUESTION What kind of classes will I take? Immunotherapy Bioinformatics at Northeastern Personalized medicine QUESTION Medical Imaging Rise of Computers = Progress Increasing Availability Gene Therapy How much will it cost me? The Future of Bioinformatics Genetic Record Keeping Important distinction between: - Bioinformatics - analyzes and organizes basic Biological data - Biological Computation - develops computational models and algorithms - Computational Biology - computational models of Biological systems Bioinformatics - Pharmacogenomics - the study of how an individual's genetic inheritance affects their response to drugs - Drug therapy and dosage prescriptions based on a genetic profile Sources Functional Genomics Do I need a background in biology AND computer scinece? Any Questions? QUESTION History of Bioinformatics in Genetic Recording A new approach to preventing and treating diseases by changing the expression of human genes using nucleic acid polymers. QUESTION Before computers, progress in genetic record keeping was relatively slow Bioinformatics - the integration of computer and information science into the biological field Sources
Transcript: the amount of available data of DNA sequences has increased exponentially since Sanger in the 1970s Sequence analysis : Bioinformatics 1970 Paulien Hogeweg "The study of informatic processes in biotic systems" Genomic revolution use of nucleotide & amino acid sequence databases Storing, Organizing and Analyzing biogical data Develop software tools Using DNA data to evaluate the evolutionary change of a species over time Build models of evolutionary systems AACAGGGCCCAGATC ----CTGGGCCCAGATC random alignment calculate its score repeat until convergence AACAGGGCCCAGATC CTGGGCCCAGATC---- AACAGGGCCCAGA----TC CTGGGC----CCAGATC---- Gibbs sampling Markov Chain Monte Carlo Sequence analysis Genome annotation Analysis of mutations in cancer Comparative genomics Computational evolutionary biology CTGGGCCCAGATC Computational evolutionary biology Some applications : find similar patterns in different sequences to : spot the active sites understand the effects of a protein predict the structure of a protein phylogenetics Phylogenetics Intro : looking for an evolutionarily related substring of width W in each sequence Frederick Sanger Nobel prize for chemistry 1958 & 1980 AACAGGGCCCAGATC
Transcript: A string of processes organised in such a way, that the output of one is the input of another In NGS, we create data that is very fragmented and noisy when compared to the previous standard of Sanger sequencing. As such, data must be processed through a bioinformatics pipeline What we will cover Currently assessing GOS pipeline. This consists of: FastQC step Alignment with BWA Mark duplicates (Picard) Recalibrate quality scores (GATK) Variant Calling (FreeBayes/GATK) Annotation (Alamut Batch) Presentation in GOSH G2P Stages of a pipeline The different ways we can process NGS data What we do at the IoN What we plan to do in the future Two main types of alignment algorithm string matching hash-based What steps are included in a pipeline? GOSH G2P Illumina sequencing produces fragmented, paired-end sequence, usually around 150bp long. In order to make sense of it, we need to identify where in the genome each sequence belongs. We do this using algorithms to match the fragments to a known reference. Bioinformatics for Beginners Also need to include a few more steps for QC etc. Heuristic variant calling Bayesian variant calling Alignment Variant Calling Annotation Data Presentation Alignment The data is then filtered and presented Filtered on: Previous classifications Frequency Prioritised on gene of interest Presented using Excel, Word or a graphical user interface (GUI) What do we do? What is a pipeline? Add additional information, for example which gene, any protein changes, frequency data etc. To assist in the interpretation of any variants identified. To do this we can access live databases or download our own versions. Once the sequence is matched to the known reference we can then look for differences in the sequence. As NGS sequencing is still not exact, we look for differences based on probability Any questions? What will we do? Annotation GOSH G2P Variant Calling QC check using FASTQC Quality Trim Novalign (hash-based) Mark duplicates (Picard Tools) Recalibrate quality scores (GATK) Call variants in batches of 24 (VarScan) Split into variants for individual samples Annotation (VEP & internal databases) Data is presented in Excel - one coverage, one variants Data Presentation
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