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Free Powerpoint Templates For Bioinformatics

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Rust for Bioinformatics

Transcript: Rust for Bioinformatics 07/06/2022 Rory Munro Rust Rust Compiled language Python interpreted Complex Why? Why Most loved language 6 years Fast Statically typed Compiler Checked/Safe Fearless Concurrency Energy Efficient Brilliant memory management (if you are a computer) No garbage collection (borrow checker) Clippy (mean crate) Cargo - think PyPI Reasons to not Why not Not chill Young - lacking utility libraries So not chill (ownership) Slower to develop in - python quick and dirty An example Example Simulating minKNOW Simulating MinKNOW Why Simulate Why simulate 1. Expensive Save time Don't real real experiments Get actual interaction rather than playback 2. Development Hackathon Python based simulator - too slow for promethion scale Works though so rewrite in rust 3. Hackathon Icarust Icarust - A Rust Based simulator Rust is fast Basis An ambitious introductory project Tonic is the fastest GRPC library Fully featured libraries available Ideology Cons A literal nightmare Doesn't work WHAT'S NEXT WHAT'S NEXT Fix rewrite bug Release Document

Bioinformatics

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!

Bioinformatics

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

PowerPoint Game Templates

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.

Bioinformatics

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

Bioinformatics for Beginners

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

Bioinformatics

Transcript: Salary range GeneStudio, Inc. Biomax Bioinformatics- computerized analysis of biological data: the use of computers to extract and analyze biological data, especially in studying the nucleotide sequences of DNA and other nucleic acids Experience 6months: yearly income $73,171 Experience 3 years: yearly income $83,251 Experience 5-9 years: yearly income $119,174 experience 15+years: yearly income $155,866 (cc) photo by Metro Centric on Flickr GeneStudio, Inc.P.O. Box 857Suwanee, GA 30024-0857U.S.A. Salaries are fairly high for those who work in bioinformatics, even those who are just entering the field. There is a great increase in salary that comes with experience. Even with just a few years of experience, the average income of a random sample of bioinformatics employees goes into the range of six figures. (NASDAQ:ACCL), a leading scientific enterprise R&D software and services company, supports industries and organizations that rely on scientific innovation to differentiate themselves. Accelrys’ Enterprise R&D Architecture, built on the industry leading Pipeline Pilot™ platform, enables customers to access, organize, analyze and share scientific data in unprecedented ways, ultimately enhancing innovation, improving productivity and compliance, reducing costs and speeding time from lab to market Education in Bioinformatics Accelrys Smarter science. Better business. Entry-level jobs in Bioinformatics Technology often require a 2-year associate or 4-year bachelor degree, but more advanced positions are usually only available to those with a master degree or doctorate, which can take up to four additional years to obtain. Students interested in Bioinformatics Technology should take classes on subjects like computer science, biology, physiology, genetics, chemistry and microbiology. Necessary Skills for a Career in Bioinformatics Technology -Bioinformatics Technicians must have a strong math and science background and need to possess advanced computer skills. They should also be detail-oriented and capable of collecting and analyzing large amounts of data. 5+7= a software company developing modern, intelligent, user-friendly, and affordable programs for molecular biologists was incorporated in 1999. Currently, our programs target the Windows platform only (cc) photo by Metro Centric on Flickr (cc) image by anemoneprojectors on Flickr Robert-Koch-Str. 2D-82152 PlaneggGermany Phone: +49 89 895574-0Fax: +49 89 895574-825Email: info@biomax.com Accelrys, Inc.10188 Telesis Court, Suite 100 San Diego, CA 92121, USA (cc) photo by jimmyharris on Flickr (cc) photo by Franco Folini on Flickr

templates for comm1500

Transcript: Conestoga Students Inc. is the student association that represents 9500+ full time students. We provide services, representation and activities for our students. As the CSI President it is my job to ensure that every single one of our students on all of Conestoga’s Campuses is represented. CSI has dedicated these past two years to creating a community throughout the college. College is the most important time in a person’s life, it is a place where you go to learn, grow and start your future. I am so proud to be part of an organization that truly stands for students, their rights, their experiences, and their growth. Creating a community is not just about joining all of the campuses together; it is about the mindset that when a student hears Conestoga they automatically think “I am Conestoga”. This has been our goal since I have been in this role, to start hearing students talk proudly about their college and know they are walking the halls of one of the best in the Country. I have been lucky to be placed in this role as President and I look forward to finishing my term this year strong and leaving knowing that each student thinks only good things when they think about Conestoga and I will know CSI was a big part in that. Activities Ciara Byrne An Oral Presentation Project on Introducing a Guest Speaker An informed organization that has comprehensive knowledge of the entitlements, processes, and services of the college and other organization's partner that link students involvement to the college, an organization and a community. A representative of student to college and the community. presented to 40 years serving students CSI Mission : Competencies Services Representation - Ciara Byrne - an official student association managed by group of leaders representing the voice of 9,500+ full time students of the College. From the desk of the CSI President : founded in 1973. a support body of students to represent in-campus and out campus activities such as social, sports, forums and conferences. The Birth of CSI. To enhance student satisfaction through active college and community awareness. Conestoga Students Inc. Professor Heather Wright Communication 1500 Good Afternoon, CSI’s Plan for Christmas Holidays: We are holding the Christmas wish tree campaign again, where students can sign up their children to receive gifts from sponsors. The sponsors are other students who come in and pick a child and ourchase gifts for them. For other activities you will have to contact becky saba at rsaba@conestogac.on.ca Who Inspired me to run for CSI: This started in my first year of college I was with a friend in my program and she said she was going to run for a director position. I wanted to get involved and I thought CSI would be the best way possible. From there I started to understand how important CSI is to the student experience and this passion of student leadership and advocacy started to grow in me. I ran for president because I wanted to make change fro the students, I wanted to serve them and work hard at giving them what they wanted. I am a firm believer in students making their own future and this position allows me to help those students who want to, to make a change in their college community How to take over for my position: Any student can run to be president of CSI, this is done through an interview process in front of the board of directors. The candidate would fill out a nomination package, the CRO would then make sure they meet the eligibility criteria and then they would present a plan/speech in front of the board and go through an extensive question process. All students are members of CSI currently, all full time students can take advantage of the services we provide. In order to run, I always encourage all students who feel that they want to make a difference for the college and our students to put their name in the hat. Anyone can do this job, it is a great learning experience for whatever program you are in that’s the beauty of it. As long as you are passionate, and here for the students you are a perfect fit to take over this -Ciara Byrne

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