Micro Binfie podcast

#Science #Micro Binfie #Microbial Bioinformatics

22:08

Host Francesca Amiker sits down with directors Joe and Anthony Russo, producer Angela Russo-Otstot, stars Millie Bobby Brown and Chris Pratt, and more to uncover how family was the key to building the emotional core of The Electric State . From the Russos’ own experiences growing up in a large Italian family to the film’s central relationship between Michelle and her robot brother Kid Cosmo, family relationships both on and off of the set were the key to bringing The Electric State to life. Listen to more from Netflix Podcasts . State Secrets: Inside the Making of The Electric State is produced by Netflix and Treefort Media.…

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Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics. The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics. Intro music : Werq - Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/ Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/ Question and comments? microbinfie@gmail.com

141 episodes

Micro binfie podcast

updated about a year ago

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141 episodes

#Science #Micro Binfie #Microbial Bioinformatics

All episodes

1
138 Decoding Tetracycline Resistance in MRSA 11:24

11 weeks ago11:24

11:24

In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, for an engaging conversation with special guest Megan Phillips, a PhD student from Emory University. Megan delves into her research on Staphylococcus aureus (MRSA), highlighting its fascinating dual nature as both a harmless and potentially serious pathogen. Megan discusses the complexities of tetracycline resistance, particularly focusing on plasmid-mediated mechanisms involving the pt181 plasmid. She explains how this plasmid’s efflux pump, encoded by the gene tetK, contributes to variable resistance levels and the factors influencing MIC (Minimum Inhibitory Concentration) variability. Listeners will learn about the intricacies of plasmid copy numbers, their global spread across clonal complexes, and the occurrence of horizontal and vertical gene transfer. Throughout the episode, Megan shares insights on working with short-read sequencing data and the strategies she employs to detect plasmid presence using tools like BLAST. She also touches on the challenges and fascinating discoveries of tracking historical sample data and integrating findings from older research papers, showcasing her appreciation for the poetic style of scientific writing from the 1940s. For those interested in antimicrobial resistance, evolutionary microbiology, and the subtleties of bacterial genome analysis, this episode offers a compelling blend of technical details and engaging storytelling. Tune in to hear more about Megan’s upcoming publications, her experiences navigating complex genomic data, and her thoughts on antimicrobial stewardship and historical perspectives on drug resistance.…

1
137 Contagion part 2 32:26

14 weeks ago32:26

32:26

In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up the virus's spread and the response to it, and that decisions about managing a crisis are based on societal values, not just science. In part one, the hosts discuss the movie's depiction of the R0 value. They note that while this explanation is useful for the audience, it is unlikely that an epidemiologist would need to explain this concept to other epidemiologists. The group notes that the MEV1 virus is modeled on the real-life Nipah virus and comment on a scene where the genome of the virus is described as being 15 to 19 kilobases in length with 6 to 10 genes. They also discuss the movie's depiction of virus isolation and the unrealistic speed with which the initial assessment of the virus occurs. The podcasters touch upon the BSL4 lab and how the film depicts how the scientists behave. They also discuss the character of Matt Damon, who is exposed to the virus but does not get sick, and is an example of an asymptomatic carrier. In part two, the bioinformaticians examine the "genome dashboard" scene, noting the software's informative interface, which includes an alignment panel, protein structure, and a recombination map. They also discuss a scene where a phylogenetic tree is used to determine a change in the R0 value. They find this unrealistic because the tree is just a picture that doesn't accurately represent how a virus spreads. The group discusses how the bioinformatician is depicted in the film as moving in and out of the lab, which may have been realistic in 2011 but is less so in the present day. They discuss how the CDC is portrayed in the film, noting scenes that were filmed at the actual CDC, as well as their experiences at the CDC. The podcasters note the movie is very US-centric and that many international partners would be involved in solving a global pandemic.…

1
135 Assembling ATCC bacterial strains 13:35

15 weeks ago13:35

13:35

In this episode of the Micro Binfie podcast, host Andrew Page is joined by Nikhita Puthuveetil, Senior Bioinformatician at the American Type Culture Collection (ATCC). They delve into ATCC's ambitious project of sequencing a vast array of organisms from their renowned collection, tackling the challenges of assembling complex genomes from bacteria, viruses, fungi, and more. Discover how Nikhita and her team navigate through genomic roadblocks, leverage cutting-edge sequencing technologies, and work to ensure accurate data provenance. Whether it's large viral genomes or evolving taxonomy, this episode offers a deep dive into the fascinating world of microbial bioinformatics and genomic curation.…

1
136 Contagion part 1 30:43

16 weeks ago30:43

30:43

1
133 The Role of Bioinformatics in Public Health and Disease Outbreaks 12:36

17 weeks ago12:36

12:36

In this episode of the Micro Binfie podcast, host Andrew Page talks with Dr. Erin Young, a bioinformatician at the Utah Public Health Laboratory, recorded during the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. Erin shares her journey from researching hereditary cancer predisposition to her current role in public health bioinformatics, which she entered through a prestigious CDC and APHL fellowship. The conversation delves into her work with bacterial pathogens, particularly in tracking antimicrobial resistance in organisms like Klebsiella. Erin discusses the tools she uses for genome typing, such as MASH, FastANI, and SKA, and her innovative research on the accuracy of long-read sequencing technologies like Nanopore for detecting antimicrobial resistance genes. She also provides a preview of her upcoming poster for ASM, where she examines how Nanopore reads can be used effectively in public health microbiology. This episode offers a fascinating look at how bioinformatics and genomics are advancing the fight against infectious diseases.…

1
134 Diving into MRSA, Genomics, and Public Health 13:27

17 weeks ago13:27

13:27

In this episode of the Micro Binfie Podcast, host Andrew Page speaks with Dr. Brooke Talbot, a recent PhD graduate from Emory University, about her research on Staphylococcus aureus, with a focus on MRSA and antibiotic resistance. Brooke shares insights into her molecular epidemiology work, discussing the complexities of tracking resistant bacterial strains in clinical settings and the significance of genomic epidemiology in public health. From honeybees to foodborne outbreaks, Brooke’s diverse research background offers listeners a fascinating journey through science, microbiology, and epidemiology.…

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132 Unlocking the Secrets of Antimicrobial Resistance in Metagenomes 11:02

19 weeks ago11:02

11:02

In this episode of the Micro Binfie podcast, host Andrew Page is live from the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. He sits down with David Mahoney, a PhD student from Dalhousie University in Halifax, Nova Scotia. David shares his research on characterizing antimicrobial resistance (AMR) genes and their transfer within metagenomes, focusing on metagenomic assembly graphs. They delve into David’s background in food safety microbiology and his interest in the public health implications of genomics. He explains his exciting work on analyzing how AMR genes transfer across different environments, such as food production plants and clinical settings, using both new and existing data from Canada’s Genomics Research and Development Initiative. David also highlights his use of innovative methods like assembly graphs and graph-based approaches to uncover AMR gene flow and lateral gene transfers, including the potential of machine learning techniques such as graph convolutional neural networks.…

1
131 Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global Genomics 12:47

21 weeks ago12:47

12:47

In this episode of the Micro Binfie Podcast, host Andrew Page catches up with Torsten Seemann at the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. They discuss the rapid evolution of bioinformatics, the challenges faced by labs worldwide, and the explosion of tools post-COVID. Torsten shares insights into his work at Melbourne’s Microbiological Diagnostic Unit (MDU), the development of platforms like OzTracker for bacterial genomics, and how his lab plays a national and international role in data sharing. The conversation dives into the future of the widely-used variant calling tool Snippy, as Torsten reveals exciting updates funded by the Chan Zuckerberg Initiative, including nanopore read support and the ability to process pre-assembled genomes. They also explore the importance of maintaining open-source bioinformatics tools to prevent them from becoming obsolete. Tune in for an in-depth discussion on the state of genomics, software development, and the challenges and rewards of open-source collaboration.…

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130 Exploring Genomic Innovation and Machine Learning in Public Health 12:35

23 weeks ago12:35

12:35

In this episode of the Micro binfie Podcast, host Andrew Page sits down with Tim Dallman at the 10th Bioinformatics Hackathon in Bethesda, Maryland. Tim shares insights from his work at Utrecht University in the Netherlands, where he focuses on genomic surveillance and machine learning models to predict disease risk and severity. They discuss the challenges of integrating genomic variation into predictive models, the importance of high-quality metadata, and the complexities of working with pathogens like Shiga toxin-producing E. coli. Tim also talks about his role at the WHO Pandemic and Epidemic Intelligence Hub and how global collaboration can drive innovation in public health genomics. Tune in to hear about cutting-edge research, the importance of interdisciplinary teamwork, and how genomic data can be harnessed for future pandemic preparedness.…

1
129 Genomics on the Frontier: Bactopia, Bioinformatics, and Pathogen Surveillance with Robert Petit 14:58

25 weeks ago14:58

14:58

Host Andrew Page is joined by Robert Petit from the Wyoming Public Health Laboratory. Robert, a key developer of the Bactopia pipeline, shares insights into how this end-to-end tool is transforming bacterial genomic surveillance. They dive into the origins of Bactopia, its applications in public health, and Robert's experience leading genomic projects in a rural setting. Discover how Bactopia streamlines pathogen detection, improves documentation, and integrates with other tools to deliver fast and accurate results. Listen in as they discuss new innovations in bioinformatics, including visualizations and human-read filtering, and explore future projects like CamelHUMP, designed to simplify sequence-based typing. Recorded live at the Microbial Bioinformatics Hackathon in Bethesda, Maryland, this episode brings you the latest in pathogen genomics and the challenges and rewards of working on the frontier of public health.…

1
128 Haiti cholera outbreak with Christine Lee and Cynney Walters 21:57

28 weeks ago21:57

21:57

Andrew and Lee talk with Christine and Cynney about the Haiti cholera outbreak Cynney Walters: https://www.linkedin.com/in/cynney-walters-763111190 Walters et al, "Genome sequences from a reemergence of Vibrio cholerae in Haiti, 2022 reveal relatedness to previously circulating strains" https://journals.asm.org/doi/abs/10.1128/jcm.00142-23…

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127 Minimum spanning trees 15:49

30 weeks ago15:49

15:49

Nabil and Lee have a quick chat about minimum spanning trees (MST). Eburst paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-152

1
126 Tree viz 21:21

32 weeks ago21:21

21:21

We go over tree visualizations! * Microreact https://microreact.org/,https://www.phylocanvas.gl/ * grapetree https://github.com/achtman-lab/GrapeTree * Auspice/NextStrain https://nextstrain.org/ * Taxonium https://taxonium.org/ * Itol: https://itol.embl.de/ * PhyloViz https://online.phyloviz.net/index * Phandango https://jameshadfield.github.io/phandango/#/main…

1
125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics 22:07

43 weeks ago22:07

22:07

125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics by Microbial Bioinformatics

1
124 Kostas Konstantinidis talks to us about ANI and metagenomics 22:58

45 weeks ago22:58

22:58

We talk with Kostas! For more information please visit https://enve-omics.gatech.edu/

Micro binfie podcast

1
123 The Revolution of Hash Databases in cgMLST 17:42

1 year ago17:42

17:42

In this episode of the Micro Binfie Podcast, hosts Dr. Andrew Page and Dr. Lee Katz delve into the fascinating world of hash databases and their application in cgMLST (core genome Multilocus Sequence Typing) for microbial bioinformatics. The discussion begins with the challenges faced by bioinformaticians due to siloed MLST databases across the globe, which hinder synchronization and effective genomic surveillance. To address these issues, the concept of using hash databases for allele identification is introduced. Hashing allows for the creation of unique identifiers for genetic sequences, enabling easier database synchronization without the need for extensive system support or resources. Dr. Katz explains the principle of hashing and its application in genomics, where even a single nucleotide polymorphism (SNP) can result in a different hash, making it a perfect solution for distinguishing alleles. Various hashing algorithms, such as MD5 and SHA-256, are discussed, along with their advantages and potential risks of hash collisions. Despite these risks, the use of more complex hashes has been shown to significantly reduce the probability of such collisions. The episode also explores practical aspects of implementing hash databases in bioinformatics software, highlighting the need for exact matching algorithms due to the nature of hashing. Existing tools like eToKi and upcoming software are mentioned as examples of applications that can utilize hash databases. Furthermore, the conversation touches on the concept of sequence types in cgMLST and the challenges associated with naming and standardizing them in a decentralized database system. Alternatives like allele codes are mentioned, which could potentially simplify the representation of sequence types. Finally, the potential for adopting this hashing approach within larger bioinformatics organizations like Phage or GMI is discussed, with an emphasis on the need for a standardized and community-supported framework to ensure the longevity and effectiveness of hash databases in microbial genomics. This episode provides a comprehensive overview of how hash databases can revolutionize microbial genomics by solving long-standing issues of database synchronization and allele identification, paving the way for more efficient and collaborative genomic surveillance worldwide.…

Micro binfie podcast

1
122 GAMBIT: Genomic Approximation Method for Bacterial Identification and Tracking 17:29

1 year ago17:29

17:29

We discuss GAMBIT, software for accurately classifying bacteria and eukaryotes using a targeted k-mer based approach. GAMBIT software: https://github.com/gambit-suite/gambit GAMBIT suite: https://github.com/gambit-suite GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. https://doi.org/10.1371/journal.pone.0277575 TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2023.1198213/full…

Micro binfie podcast

1
121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown 20:03

1 year ago20:03

20:03

In this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, diving deeper into his work on k-mers, Sourmash, and open source software development: Topics discussed: K-mers for analyzing sequencing data, and how Sourmash builds on MinHash How Sourmash handles k-mers for metagenomic comparisons vs. MASH The modhash and bottom sketch approaches used in Sourmash Dealing with sequencing errors and noise in k-mer data Sourmash as a reference-based method, and applications for metagenomics Titus' focus on building reusable libraries and APIs vs one-off tools Recruiting collaborators through "nerd sniping" with interesting problems The open source philosophy that motivates Titus' software work Overall, the conversation provides insight into Titus' approach to bioinformatics software through iterating quickly, focusing on usability, and building open source tools. Papers: Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4 Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2 IBD exploration - https://dib-lab.github.io/2021-paper-ibd/…

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1
120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown 25:25

1 year ago25:25

25:25

In this final episode with Titus Brown, the conversation focuses on his work scaling metagenomic search with Sourmash: An overview of what Sourmash does - sketching and comparing large k-mer datasets How the sampling approach enables analyses like containment estimation Exciting capabilities of the Branchwater tool for multi-threaded real-time SRA search Scaling to search across millions of metagenomes in seconds with WebAssembly Potential public health applications for tracking and sourcing pathogens Important caveats around resolution limits and need for follow-up analyses Ongoing work to characterize the technique's specificity and sensitivity Overall, this episode highlights the massive scaling Sourmash enables for metagenomic search, and the potential use cases in public health, while acknowledging current limitations and uncertainties. Titus emphasizes the need to precisely convey what bioinformatic tools can and cannot do as research continues. Papers: Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4 Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2 IBD exploration - https://dib-lab.github.io/2021-paper-ibd/…

Micro binfie podcast

1
119 The Challenges of Microbial Taxonomy - Conversations with Titus Brown 22:53

1 year ago22:53

22:53

In this episode, Andrew Page and Lee Katz continue their chat with Titus Brown, focusing on taxonomy assignment in metagenomics: Topics discussed: Dealing with contamination and low quality genomes in reference databases Sourmash as a versatile search tool, not a curated database The need for high confidence in taxonomic assignment in public health Most microbial assignment tools have low specificity or sensitivity Possible ways to achieve perfect species classification (in theory) The challenges around defining species based on small genomic differences Interesting cryptography concept of 'unicity' distance for classification Conveying the nuances and uncertainties in taxonomic assignment The conversation highlights the difficulties around taxonomic classification, especially at the species level, but explores ideas for improving accuracy. Overall it emphasizes the complexities of biology and need for transparent conveyance of uncertainties. Papers: Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4 Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2 IBD exploration - https://dib-lab.github.io/2021-paper-ibd/…

Micro binfie podcast

1
118 Real bioinformaticians react to Jurassic Park 1:00:44

1 year ago1:00:44

1:00:44

Andrew, Nabil, and Lee react to the bioinformatics and the science overall in the 1993 film Jurassic Park. We looked at these YouTube clips: * https://youtu.be/mDTaykXudVI?si=I5aiUdBGStpIKHVC * https://youtu.be/RLz5Api676Y?si=D6nps33O42Fmk4Ac * https://youtu.be/0Nz8YrCC9X8?si=KNwkeFoS6Bu4LOpv * https://youtu.be/dxIPcbmo1_U?si=TOBw5AONYVCW0JzV * https://youtu.be/m1lc8GwBKFE?si=rj7Oiq51l2_dB6ro More information on the secret tattoo here: https://underunderstood.com/podcast/episode/jeff-goldblums-secret-tattoo-jurassic-park-ian-malcolm/…

Micro binfie podcast

1
117 From Math to Metagenomics - Titus Brown on Career Journeys and Software Solutions 20:12

1 year ago20:12

20:12

In this episode of the Micro Binfie Podcast, Andrew Page and Lee Katz interview Titus Brown about his journey from studying math and physics as an undergrad to becoming a bioinformatician focusing on metagenomics and software development. Topics discussed: Titus' background in math, physics, digital evolution research, and developmental biology His transition into bioinformatics to analyze the influx of genomic data in the 1990s Developing early tools for comparative genomics and sequence analysis The philosophy of creating usable software with good documentation Work on transcriptomics, metagenomics, and k-mers at Michigan State Digital normalization and dealing with large sequencing datasets Moving to UC Davis and continuing work on metagenomics and software like khmer and sourmash Thoughts on challenges around data reuse and accessibility in science. Papers: Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4 Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2 IBD exploration - https://dib-lab.github.io/2021-paper-ibd/…

Micro binfie podcast

1
116 AI Authorship and Ethics in Academic Publishing for Genomics 32:27

1 year ago32:27

32:27

The podcast discusses an article co-authored by Andrew Page, examining the use of GPT-4 for research publication. The conversation focuses on the authorship of articles generated by GPT-4 and the implications for academic publishing. Authorship and Ethics: Andrew discusses the question of authorship when AI-generated content is involved in research articles. He explores the ethical implications and potential biases associated with AI-assisted writing, such as the omission of minority figures and novel discoveries. He emphasizes the importance of transparency when using AI and its potential to democratize research, as long as ethical guidelines are maintained. AI & Scientific Journals: The podcast delves into the current landscape of AI in academic publishing. It addresses the commercial use of AI in crafting manuscripts for research articles and the necessity of distinguishing between manual and AI-generated contributions. The possible misalignment of GPT-4's commercial objectives with academic goals is highlighted. Risks and Benefits: Andrew outlines the risks of using AI in publishing, such as unintentional plagiarism, biases, and outdated methods. He provides an example of bioinformatics software recommending deprecated methods, illustrating the need for caution. The conversation also touches upon the AI's potential to introduce bias unintentionally, citing past incidents where AI models quickly adopted extremist views. Andrew's co-authors, Niamh Tumelty and Sam Sheppard, bring different perspectives on ethics and the impact of AI on publishing. Niamh, associated with the London School of Economics, emphasizes ethical considerations, while Sam, editor-in-chief of Microbial Genomics, underscores the need to adapt to the reality of AI contributions in journal submissions. In conclusion, the podcast underscores the importance of recognizing and navigating the ethical challenges posed by AI in academic publishing. It suggests that the technology may evolve faster than policies can adapt, necessitating an ongoing conversation among researchers, publishers, and AI developers. Links: https://microbiologysociety.org/blog/microbe-talk-ai-a-useful-tool-or-dangerous-unstoppable-force.html https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001049…

Micro binfie podcast

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115 Write-the: speeding up software development for bioinformatics 24:22

1 year ago24:22

24:22

We continue our conversation with Wytamma Wirth about write-the and all things AI. It starts with discussing the usage of language models, specifically ChatGPT, in writing boilerplate code, and how it can assist in generating code snippets, unit tests, and even documentation strings. The participants also explore the potential of incorporating it into code editors to make coding more efficient and less error-prone. The conversation then shifts to discuss the generation of research papers, specifically software announcements, by leveraging code documentation. The participants believe ChatGPT could be useful in generating introductions and backgrounds for such publications. They also touch upon the utility of language models in translating documentation into different human languages to assist non-native English speakers. The discussion returns to code documentation, focusing on the tool "write the docs" which auto-generates well-structured and searchable documentation websites. The participants appreciate the tool's ease of use and the potential it has in maintaining proper documentation for projects. The conversation ends with an acknowledgment of the importance of human oversight in automating tasks using language models. Links: Write-the software: https://github.com/Wytamma/write-the Wytamma Wirth: https://www.wytamma.com/…

Micro binfie podcast

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114 Write-the: Automating Code Documentation ChatGPT 25:35

1 year ago25:35

25:35

In this episode, we dive deep into the world of automated code documentation and conversion using ChatGPT through the write-the software developed by Dr Wytamma Wirth from The University of Melbourne. Our guest, an experienced software engineer, takes us on a journey through the challenges and nuances of writing code documentation and the role AI can play in easing this process. We explore the intersection of ChatGPT's capabilities with Write the Docs, a documentation system widely used by developers. From highlighting ChatGPT's ability to understand and generate code snippets, to demonstrating real-time code conversion across multiple programming languages, this episode is a treasure trove for developers looking to enhance their workflow. Whether you're a seasoned developer or just getting started, tune in to discover how the synergy of AI and coding can elevate your documentation game to the next level! Links: Write-the software: https://github.com/Wytamma/write-the Wytamma Wirth: https://www.wytamma.com/…

Micro binfie podcast

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113 Global Microbial Identifier conference with Ruth Timme 8:11

2 years ago8:11

8:11

Lee and Andrew are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. On day 3 we catch up with Dr Ruth Timme.

Micro binfie podcast

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112 Global Microbial Identifier conference with Will Hsiao 7:35

2 years ago7:35

7:35

Andrew and Lee are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. We talk to Dr William Hsiao, one of the organisers of the conference.

Micro binfie podcast

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111 Global Microbial Identifier with Finlay Maguire and Emma Griffiths 21:08

2 years ago21:08

21:08

Andrew and Lee are at the Global Microbial Identifier conference 13 in Vancouver Canada. On the first day they talked to Dr Finlay Maguire and Dr Emma Griffiths about microbial genomics and Tim Hortons.

Micro binfie podcast

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110 ChatGPT: The Bioinformatics Calculator 26:47

2 years ago26:47

26:47

In this episode there is a comprehensive discussion on the influence of AI, especially GPT-4, in the sphere of microbial bioinformatics. They reflect on a study testing GPT-4's problem-solving capabilities, which raises concerns about its potential impact on employment practices and academic integrity. There's speculation that AI's proficiency in tackling standard technical problems could interfere with genuinely evaluating a candidate's knowledge during interviews. Drawing parallels with calculators, the hosts deliberate on whether AI tools should be permitted during assessments. They stress the necessity for individuals to possess a deep understanding of their domain to accurately interpret and validate AI solutions. Discussing the AI's limitations, the hosts highlight its struggles with regular expressions and handling larger scripts. They observe the AI tends to loop and repeat itself, performing better with shorter scripts but faltering on more complex tasks often seen in bioinformatics. This prompts a discussion on how educators should address these developments in their teaching strategies. Moreover, the hosts explore the potential of large language models to improve base calling and read correction in sequencing, drawing on the structured and predictable nature of language and genetic code. They also discuss the idea of introducing randomness in these models to generate creative and varied solutions, potentially predicting future alleles or gene configurations. Ultimately, they express a blend of enthusiasm and apprehension towards the swift advances in this field and the ensuing implications for bioinformatics. They end on a note of anticipation for future developments, with a humorous nod towards AI's potential for automating mundane tasks like auto-correcting sample sheets. References: What Is ChatGPT Doing … and Why Does It Work? https://writings.stephenwolfram.com/2023/02/what-is-chatgpt-doing-and-why-does-it-work/ Many bioinformatics programming tasks can be automated with ChatGPT https://arxiv.org/ftp/arxiv/papers/2303/2303.13528.pdf ChatGPT for bioinformatics https://medium.com/@91mattmoore/chatgpt-for-bioinformatics-404c6d0817a1 Empowering Beginners in Bioinformatics with ChatGPT https://www.biorxiv.org/content/10.1101/2023.03.07.531414v1 Lawyer uses GPT and get ethics violation https://simonwillison.net/2023/May/27/lawyer-chatgpt/ Can ChatGPT solve bioinformatic problems with Python? https://dmnfarrell.github.io/bioinformatics/chatGPT-python…

Micro binfie podcast

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109 AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics 30:56

2 years ago30:56