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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 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 ...
 
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 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 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…
 
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…
 
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…
 
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 …
 
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…
 
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 …
 
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 …
 
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…
 
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…
 
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…
 
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…
 
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…
 
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…
 
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…
 
NGLess is a programming language specificallytargeted at next generation sequencing (NGS) data processing.In this episode we chat with its main developer, Luis PedroCoelho, about the benefits of domain-specificlanguages, pros and cons of Haskell in bioinformatics, reproducibility, and ofcourse NGLess itself. Links: NGLess on GitHub NG-meta-profiler…
 
Summary Once you release an application into production it can be difficult to understand all of the ways that it is interacting with the systems that it integrates with. The OpenTracing project and its accompanying ecosystem of technologies aims to make observability of your systems more accessible. In this episode Austin Parker and Alex Boten exp…
 
Conversation with Dan VahdatThe ninth episode brings you ever closer to the future of healthcare with Thomas discussing the possibilities of digital biomarkers for modern medicine with Dan Vahdat, founder and CEO of Huma (formerly: Medopad). Together, they shed light on the prospect of diagnosing diseases in the earliest stages and how this contrib…
 
Summary Our thought patterns are rarely linear or hierarchical, instead following threads of related topics in unpredictable directions. Topic modeling is an approach to knowledge management which allows for forming a graph of associations to make capturing and organizing your thoughts more natural. In this episode Brett Kromkamp shares his work on…
 
Summary You spend a lot of time and energy on building a great application, but do you know how it’s actually being used? Using a product analytics tool lets you gain visibility into what your users find helpful so that you can prioritize feature development and optimize customer experience. In this episode PostHog CTO Tim Glaser shares his experie…
 
Summary The divide between Python 2 and 3 lasted a long time, and in recent years all of the new features were added to version 3. To help bridge the gap and extend the viability of version 2 Naftali Harris created Tauthon, a fork of Python 2 that backports features from Python 3. In this episode he explains his motivation for creating it, the proc…
 
In this episode, I continue to talk (but mostly listen) to Sergey Koren and Sergey Nurk.If you missed the previous episode, you should probably start there.Otherwise, join us to learn about HiFi reads, the tradeoff between read lengthand quality, and what tricks HiCanu employs to resolve highly similar repeats. Links: HiCanu: accurate assembly of s…
 
Summary Dependency management in Python has taken a long and winding path, which has led to the current dominance of Pip. One of the remaining shortcomings is the lack of a robust mechanism for resolving the package and version constraints that are necessary to produce a working system. Thankfully, the Python Software Foundation has funded an effor…
 
In this episode Sergey Nurk and Sergey Koren from the NIH share their thoughtson genome assembly. The two Sergeys tell the stories behind their amazingcareers as well as behind some of the best known genome assemblers: Celeraassembler, Canu, and SPAdes. Links: Canu on GitHub SPAdes on GitHubBy Roman Cheplyaka
 
Summary One of the most common causes of bugs is incorrect data being passed throughout your program. Pydantic is a library that provides runtime checking and validation of the information that you rely on in your code. In this episode Samuel Colvin explains why he created it, the interesting and useful ways that it can be used, and how to integrat…
 
Summary More of us are working remotely than ever before, many with no prior experience with a remote work environment. In this episode Quinn Slack discusses his thoughts and experience of running Sourcegraph as a fully distributed company. He covers the lessons that he has learned in moving from partially to fully remote, the practices that have w…
 
Conversation with Dr. Johannes WimmerWhile COVID-19 makes it necessary for the healthcare system to increase use of digital means at the moment, this could also function as a digitization catalyst and create sustainable change. Dr. Johannes Wimmer, Germany's leading TV doctor, explains why this would be a positive outcome of the crisis in the podca…
 
Summary After you write your application, you need a way to make it available to your users. These days, that usually means deploying it to a cloud provider, whether that’s a virtual server, a serverless platform, or a Kubernetes cluster. To manage the increasingly dynamic and flexible options for running software in production, we have turned to b…
 
Porcupine is a molecular tagging system—a way to tag physicalobjects with pieces of DNA called molecular bits, or molbits for short.These DNA tags then can be rapidly sequenced on an Oxford Nanopore MinIONdevice without any need for library preparation. In this episode Katie Doroschak explains how Porcupine works—how molbitsare designed and prepare…
 
Summary Python has become a major player in the machine learning industry, with a variety of widely used frameworks. In addition to the technical resources that make it easy to build powerful models, there is also a sizable library of educational resources to help you get up to speed. Sebastian Raschka’s contribution of the Python Machine Learning …
 
Conversation with Prof. Dr. Christiane WoopenTogether with Prof. Dr. Christiane Woopen, medical ethicist and Executive Director of ceres at the University of Cologne, Thomas discusses the implications of COVID-19 for basic human rights and that health is only one of our fundamental goods, whereas freedom is the highest good from an ethical perspect…
 
Summary Python has an embarrasment of riches when it comes to web frameworks, each with their own particular strengths. FastAPI is a new entrant that has been quickly gaining popularity as a performant and easy to use toolchain for building RESTful web services. In this episode Sebastián Ramirez shares the story of the frustrations that led him to …
 
Julie Messersmith, Executive Director for Research at Johns Hopkins, discusses her roles in the strategies involved in bringing multi-disciplinary researchers together to work on COVID-19 and SARS-CoV-2. She shares information about the program for coordinated response with 9 working groups that were formed shortly after Hopkins shut down non essen…
 
Summary Distributed computing is a powerful tool for increasing the speed and performance of your applications, but it is also a complex and difficult undertaking. While performing research for his PhD, Robert Nishihara ran up against this reality. Rather than cobbling together another single purpose system, he built what ultimately became Ray to m…
 
Summary Bioinformatics is a complex and computationally demanding domain. The intuitive syntax of Python and extensive set of libraries make it a great language for bioinformatics projects, but it is hampered by the need for computational efficiency. Ariya Shajii created the Seq language to bridge the divide between the performance of languages lik…
 
Summary The state of the art in natural language processing is a constantly moving target. With the rise of deep learning, previously cutting edge techniques have given way to robust language models. Through it all the team at Explosion AI have built a strong presence with the trifecta of SpaCy, Thinc, and Prodigy to support fast and flexible data …
 
Will Townes proposes a new, simpler way to analyze scRNA-seq data with uniquemolecular identifiers (UMIs). Observing that such data is not zero-inflated,Will has designed a PCA-like procedure inspired by generalized linear models(GLMs) that, unlike the standard PCA, takes into account statisticalproperties of the data and avoids spurious correlatio…
 
Summary Running a successful business requires some method of organizing the information about all of the processes and activity that take place. Tryton is an open source, modular ERP framework that is built for the flexibility needed to fit your organization, rather than requiring you to model your workflows to match the software. In this episode …
 
In a special episode, I speak to Elodie Ghedin about the pandemic and global health crisis we are facing. Elodie is a virologist and professor at NYU in Biology and Global Public Health. She studies microbial pathogens including human parasites and viruses and has done extensive work with influenza and other RNA viruses. In this episode we talk abo…
 
Summary One of the driving factors of Python’s success is the ability for developers to integrate with performant languages such as C and C++. The challenge is that the interface for those extensions is specific to the main implementation of the language. This contributes to difficulties in building alternative runtimes that can support important p…
 
Summary Quantum computers promise the ability to execute calculations at speeds several orders of magnitude faster than what we are used to. Machine learning and artificial intelligence algorithms require fast computation to churn through complex data sets. At Xanadu AI they are building libraries to bring these two worlds together. In this episode…
 
Summary Most long-running programs have a need for executing periodic tasks. APScheduler is a mature and open source library that provides all of the features that you need in a task scheduler. In this episode the author, Alex Grönholm, explains how it works, why he created it, and how you can use it in your own applications. He also digs into his …
 
In this episode we hear from Amatur Rahmanand Karel Břinda, whoindependently of one another released preprints on the same concept, calledsimplitigs or spectrum-preserving string sets. Simplitigs offer a way toefficiently store and query large sets of k-mers—or, equivalently, large deBruijn graphs. Links: Simplitigs as an efficient and scalable rep…
 
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