show episodes
 
The Strategy& Insider podcast aims to explore some of the most critical future trends and their impacts. Strategy& talks to industry experts and leading practitioners from different sectors. The conversations will make you more familiar with key developments by providing you with insights that really matter. The first season will tackle some of the most fundamental questions in the healthcare industry. While technology has quickly transformed how we shop, bank, and travel, it yet has to impa ...
 
This course covers fundamental algorithms for efficient analysis of biological sequences and for building evolutionary trees. This is an undergraduate course focusing on the ideas and concepts behind the most central algorithms in biological sequence analysis. Dynamic Programming, Alignment, Hidden Markov Models, Statistical Analysis are emphasized.
 
The Department of Statistics at Oxford is a world leader in research including computational statistics and statistical methodology, applied probability, bioinformatics and mathematical genetics. In the 2014 Research Excellence Framework (REF), Oxford's Mathematical Sciences submission was ranked overall best in the UK. This is an exciting time for the Department. We have now moved into our new home on St Giles and we are currently settling in. The new building provides improved lecture and ...
 
EPCC and the MSc in High Performance Computing run an annual Guest Lecture series, with speakers drawn from industry and academia. Talks focus on state-of-the-art applications of HPC in real world situations, with many reflecting the type of work our MSc students will undertake after graduation.www.epcc.ed.ac.uk/msc twitter.com/#!/EPCCedinburgh
 
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show series
 
In this episode, Jacob Schreiber interviews Devin Schweppe aboutthe analysis of mass spectrometry data in the field of proteomics. They beginby delving into the different types of mass spectrometry methods, including MS1, MS2, and, MS3, and the reasons for using each. They then discuss a recent paperfrom Devin, Full-Featured, Real-Time Database Sea…
 
In this season finale episode, we discuss recent scientific news covering COVID vaccines and vaccine related jargon, results from a simulation study related to climate change and the nature communication paper describing influence of gender on mentor ship. See you soon in 2021! Email us at: computationallyyours@gmail.com Follow us on Twitter: @comp…
 
Summary In a software project writing code is just one step of the overall lifecycle. There are many repetitive steps such as linting, running tests, and packaging that need to be run for each project that you maintain. In order to reduce the overhead of these repeat tasks, and to simplify the process of integrating code across multiple systems the…
 
Summary Building a machine learning model is a process that requires well curated and cleaned data and a lot of experimentation. Doing it repeatably and at scale with a team requires a way to share your discoveries with your teammates. This has led to a new set of operational ML platforms. In this episode Michael Del Balso shares the lessons that h…
 
In light of the monumental weekend in the United States, we got thinking about women who changed Science forever, and the first name that comes up is Marie Curie. This episode highlights her fascinating story. Email us at: computationallyyours@gmail.com Follow us on Twitter: @compbiopodcast ; Dr. Sabah Kadri: @sabahkadri ; Arshi Arora: @arorarshi W…
 
Summary The CPython implementation has grown and evolved significantly over the past ~25 years. In that time there have been many other projects to create compatible runtimes for your Python code. One of the challenges for these other projects is the lack of a fully documented specification of how and why everything works the way that it does. In t…
 
In this episode, Arshi Arora takes you over a brief journey of data science and statistics in the field of Genomics. What are the steps of a typical data analysis pipeline, and some fun analogies to understand basic to complicated statistical concepts. We would love to hear from you if you think we missed something or you would like us to cover som…
 
Summary Artificial intelligence applications can provide dramatic benefits to a business, but only if you can bring them from idea to production. Henrik Landgren was behind the original efforts at Spotify to leverage data for new product features, and in his current role he works on an AI system to evaluate new businesses to invest in. In this epis…
 
Conversation with Dr. Sachin JainThis episode features Dr. Sachin Jain who is the CEO of Scan Health Plan and who used to serve in the Obama administration. This conversation is about the benefits of virtual specialty care, why we should strive for a better normal instead of a new normal and what it takes to achieve real transformation within the h…
 
In this episode Will Freyman talks about identity-by-descent (IBD): howit’s used at 23andMe, and how the templatedpositional Burrows-Wheeler transform can find IBD segments in the presence ofgenotyping and phasing errors. Links: Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform (William A. Freyman…
 
Starting this month, we will be highlighting the main news in science for the month. This month, we highlighted three main stories: 1. Nobel Prize in Chemistry for CRISPR 2. Editorial in New England Journal of medicine “Dying in a Leadership Vacuum” 3. What's new in Remdesivir news? Contradicting evidence publications and FDA approval. References c…
 
Summary Python and Java are two of the most popular programming languages in the world, and have both been around for over 20 years. In that time there have been numerous attempts to provide interoperability between them, with varying methods and levels of success. One such project is JPype, which allows you to use Java classes in your Python code.…
 
Jason Forrest, Director of Interactive Data Visualization, McKinsey and Co, New York, gives the Department of Statistics Black History Month lecture, with a talk on the work of African-American scholar and activist W.E.B. Du Bois. At the 1900 Paris Exposition, an all African-American team lead by scholar and activist W.E.B. Du Bois sought to challe…
 
In this episode of Computationally Yours, host Dr. Sabah Kadri discusses a topic she has been mulling over converting into an episode for a long time - the nuts and bolts of Bioinformatics. She introduces the field, discusses its fuzzy history and then shares nuggets of wisdom for both new and aspiring Bioinformaticians talking about things she wis…
 
Summary The release of Python 3.9 introduced a new parser that paves the way for brand new features. Every programming language has its own specific syntax for representing the logic that you are trying to express. The way that the rules of the language are defined and validated is with a grammar definition, which in turn is processed by a parser. …
 
In this new episode, hosts Arshi Arora and Dr. Sabah Kadri discuss their professional stories in Computational Biology of more than a decade. They discuss their career paths, starting from what it takes to decide that one follows a doctorate degree to doing two Masters degrees. We hope students in the field, especially women in science enjoy hearin…
 
Summary The way that applications are being built and delivered has changed dramatically in recent years with the growing trend toward cloud native software. As part of this movement toward the infrastructure and orchestration that powers your project being defined in software, a new approach to operations is gaining prominence. Commonly called Git…
 
In this episode, Jacob Schreiber interviews David Kelley aboutmachine learning models that can yield insight into the consequences ofmutations on the genome. They begin their discussion by talking about Calico Labs, and then delve into a series of papers that David haswritten about using models, named Basset and Basenji, that connect genome sequenc…
 
Summary Learning to code is a neverending journey, which is why it’s important to find a way to stay motivated. A common refrain is to just find a project that you’re interested in building and use that goal to keep you on track. The problem with that advice is that as a new programmer, you don’t have the knowledge required to know which projects a…
 
In this first of its kind episode in the field, host Dr. Sabah Kadri assembled a panel of distinguished Clinical Bioinformatics Directors for this very special episode. Dr. Eric Klee (Mayo Clinic), Dr. Ahmet Zehir (Memorial Sloan Kettering) and Dr. Matthew Hestand (Cincinnati Children's) talk about being leaders in the field, the challenges of hiri…
 
Summary Python is a powerful and expressive programming language with a vast ecosystem of incredible applications. Unfortunately, it has always been challenging to share those applications with non-technical end users. Gregory Szorc set out to solve the problem of how to put your code on someone else’s computer and have it run without having to rel…
 
Conversation with Henrik Matthies and Julia HagenFor the first time, we welcome two guests to our podcast: Henrik Matthies and Julia Hagen from the Health Innovation Hub (hih) share their insights straight out of the ,digital forge' of Germany's Federal Ministry of Health. They stress the importance of an ecosystem approach and explain how COVID-19…
 
In this episode, your hosts, Dr. Sabah Kadri and Arshi Arora bring to you united yet diverse sub fields of Computational Biology in the voice of four different scientists, spanning areas of Structural Biology, Systems Biology, Chemistry, Proteomics and Genomics. They cover their background, speciality and what drew them to Computational ability in …
 
Summary Servers and services that have any exposure to the public internet are under a constant barrage of attacks. Network security engineers are tasked with discovering and addressing any potential breaches to their systems, which is a never-ending task as attackers continually evolve their tactics. In order to gain better visibility into complex…
 
In this episode, Dr. Sabah Kadri and Arshi Arora discuss the viewpoints of 6 esteemed scientists from the latest Nature review Genetics paper celebrating 20 years. From population genetics to non-coding genome, from equity to diversity and more, this is a must listen. Paper discussed: https://pubmed.ncbi.nlm.nih.gov/32839576/ Contact us with questi…
 
Summary News media is an important source of information for understanding the context of the world. To make it easier to access and process the contents of news sites Lucas Ou-Yang built the Newspaper library that aids in automatic retrieval of articles and prepare it for analysis. In this episode he shares how the project got started, how it is i…
 
In this episode, Jacob Schreiber interviews Jill Moore aboutrecent research from the ENCODE Project. They begin theirdiscussion with an overview and goals of the ENCODE Project, and thendiscuss a bundle of papers that were recently published in variousNature journals and the flagship paper, Expanded encyclopaedias of DNA elements in the human and m…
 
Summary Data applications are complex and continually evolving, often requiring collaboration across multiple teams. In order to keep everyone on the same page a high level abstraction is needed to facilitate a cross-cutting view of the data orchestration across integration, transformation, analytics, and machine learning. Dagster is an innovative …
 
In our next “Profiles of Scientific Genius” series, we bring to you the life story of the Father of Modern Genetics, Gregor Johann Mendel (1822-1884). Dr. Sabah Kadri and Arshi Arora talk about his journey from a monk to a scientist, his iconic work on pea plants, Mendel's Laws of inheritance, and lastly a brief note about the Mendel-Fisher controv…
 
Summary The internet is a rich source of information, but a majority of it isn’t accessible programmatically through APIs or databases. To address that shortcoming there are a variety of web scraping frameworks that aid in extracting structured data from web pages. In this episode Attila Tóth shares the challenges of web data extraction, the ways t…
 
In this episode, we sat down with hosts of 5 other podcasts on pathology and science: Deeper Levels, People of Pathology, PathPod, ScopeMD, and Dead Men Do Tell Tales for a Mega crossover episode. We talk about podcasting, what got us started on this journey, what we have learned, and even share a joke. It was fun to share and learn from our fellow…
 
Summary A large portion of the software industry has standardized on Git as the version control sytem of choice. But have you thought about all of the information that you are generating with your branches, commits, and code changes? Davide Spadini created the PyDriller framework to simplify the work of mining software repositories to perform resea…
 
In systems biology, Boolean networks are a way to model interactions such asgene regulation or cell signaling. The standardinterpretations of Boolean networks are the synchronous, asynchronous, andfully asynchronous semantics. In this episode Loïc Paulevé explains how thesame Boolean networks can be interpreted in a new, “most permissive” way.Loïc …
 
In today’s episode, we reached out to four diagnostic experts across the United States to share their experiences in bringing on SARS-CoV-2 testing in their laboratories. We asked them to share the biggest challenge they faced and also share one thing with the listeners of Computationally Yours that isn’t common knowledge about this testing. Dr. Sa…
 
Summary The Musicbrainz project was an early entry in the movement to build an open data ecosystem. In recent years, the Metabrainz Foundation has fostered a growing ecosystem of projects to support the contribution of, and access to, metadata, listening habits, and review of music. The majority of those projects are written in Python, and in this …
 
In this episode, hosts, Dr. Sabah Kadri and Arshi Arora dive deep into the launch of a genetic test - what does it mean? What are the types of genetic testing? What goes into designing a genetic test? What is involved in validating this test clinically? What are the accuracy metrics? An easy listen covering a very complex topic. Contact us with que…
 
Summary Python is a leading choice for data science due to the immense number of libraries and frameworks readily available to support it, but it is still difficult to scale. Dask is a framework designed to transparently run your data analysis across multiple CPU cores and multiple servers. Using Dask lifts a limitation for scaling your analytical …
 
Summary Netflix uses machine learning to power every aspect of their business. To do this effectively they have had to build extensive expertise and tooling to support their engineers. In this episode Savin Goyal discusses the work that he and his team are doing on the open source machine learning operations platform Metaflow. He shares the inspira…
 
In this episode, Jacob Schreiber interviews Marinka Zitnik aboutapplications of machine learning to drug development.They begin their discussion with an overview of open research questions in thefield, including limiting the search space of high-throughput testing methods,designing drugs entirely from scratch, predicting ways that existing drugs ca…
 
In this episode, hosts, Dr. Sabah Kadri and Arshi Arora ask leading experts in Molecular Pathology across clinical laboratories across the United States, their personal experience with Precision Medicine, its effect on their clinical practice as well as their views of the future of personalized medicine. Ours guests for this episode are: Dr. Rashmi…
 
Summary One of the best methods for learning programming is to just build a project and see how things work first-hand. With that in mind, Ken Youens-Clark wrote a whole book of Tiny Python Projects that you can use to get started on your journey. In this episode he shares his inspiration for the book, his thoughts on the benefits of teaching testi…
 
Did you know there was a time when no one knew about blood groups so no one knew to check the blood group of a donor before transfusion? There was also a time when a patient's treatment could not be tailored to their DNA changes. But none of that happens today. Do you know why? And do you know how? Listen to Dr. Sabah Kadri break down precision med…
 
Summary Python is an intuitive and flexible language, but that versatility can also lead to problematic designs if you’re not careful. Nikita Sobolev is the CTO of Wemake Services where he works on open source projects that encourage clean coding practices and maintainable architectures. In this episode he discusses his work on the DRY Python set o…
 
Conversation with Nora BumThe tenth episode revolves around the digitization of mental healthcare. Our guest Nora Blum – founder and CEO of the German start-up Selfapy – illustrates that digital apps are a decisive tool in the treatment of mental diseases and increasingly help patients with depressions, eating disorders and other psychiatric illnes…
 
Our hosts, Dr. Sabah Kadri and Arshi Arora are women in science celebrating a friendship that spans over a decade. In this episode, we get up-close and personal to get to know our hosts, their journeys in science and the hardships along the way. They discuss what excites them about science (Spoiler alert: it's everything), an embarrassing revelatio…
 
Summary Barry Warsaw has been a member of the Python community since the very beginning. His contributions to the growth of the language and its ecosystem are innumerable and diverse, earning him the title of Friendly Language Uncle For Life. In this episode he reminisces on his experiences as a core developer, a member of the Python Steering Commi…
 
In our first "Profiles in Scientific Genius" series, we discuss the inspiring story of Dr. Barbara McClintock (1902-1992), the first woman to have received a solo Nobel Prize in Physiology or Medicine. Achieving success against all odds, her story will make you believe. Dr. Sabah Kadri and Arshi Arora peek into her childhood, her support system, th…
 
Summary Building and managing servers is a challenging task. Configuration management tools provide a framework for handling the various tasks involved, but many of them require learning a specific syntax and toolchain. PyInfra is a configuration management framework that embraces the familiarity of Pure Python, allowing you to build your own integ…
 
Our DNA makes us unique. It also makes us similar to each other - sometimes more and sometimes less. How? Dr. Sabah Kadri and Arshi Arora explore similarities and differences in our DNA. And in the process, they discuss milestone genomics projects in human beings such as dbSNP, the HapMap project and Genome Wide Association Studies. They look at st…
 
Summary Programming languages are a powerful tool and can be used to create all manner of applications, however sometimes their syntax is more cumbersome than necessary. For some industries or subject areas there is already an agreed upon set of concepts that can be used to express your logic. For those cases you can create a Domain Specific Langua…
 
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