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the bioinformatics lab
the bioinformatics labEP64: Machine Learning and Mutli-Omics Data with Mxolisi NeneIn this episode of the Bioinformatics Lab Podcast, Mxolisi Nene shares his journey from a curious kid “scanning soil” with a stick and a broken Pentium II in rural KwaZulu-Natal to a bioinformatician and PhD candidate at the Agricultural Research Council in Pretoria. He walks through his path from animal science into bioinformatics, profiling the gut microbiomes of indigenous village chickens using 16S and metagenomic sequencing, and how wrestling with messy real-world data led him into multi-omics integration and machine learning. Mxolisi explains concepts like feature engineering, neural networks, and ecological “tipping points” in soil ecosystems—showing how combining metagenomic, metabolomi...
2025-11-2059 minDataTalks.Club
DataTalks.ClubFrom Biotechnology to Bioinformatics Software - Sebastian Ayala RuanoIn this talk, Sebastian, a bioinformatics researcher and software engineer, shares his inspiring journey from wet lab biotechnology to computational bioinformatics. Hosted by Data Talks Club, this session explores how data science, AI, and open-source tools are transforming modern biological research — from DNA sequencing to metagenomics and protein structure prediction.You’ll learn about: - The difference between wet lab and dry lab workflows in biotechnology - How bioinformatics enables faster insights through data-driven modeling - The MCW2 Graph Project and its role in studying wastewater microbiomes ...
2025-10-2455 minthe bioinformatics lab
the bioinformatics labEP 63: Mycotic Bioinformatics with Zachary KonkelIn this episode of the Bioinformatics Lab Podcast, Zachary Konkel shares his journey from studying chemistry to specializing in mycology and bioinformatics. He discusses the significance of fungi in medicine, particularly in producing antimicrobial compounds, and the challenges faced in fungal genomics. Zach highlights the development of mycotools (https://github.com/xonq/mycotools) as a solution for analyzing fungal genomes and the importance of phylogenetics in understanding fungal pathogens like Candida auris. The conversation also touches on the growing concern of antifungal resistance and the potential for next-generation sequencing to improve outbreak detection. Finally, Zach shares his passion for mushroom...
2025-10-221h 08the bioinformatics lab
the bioinformatics labEP 62: Public Health Pathogen Genomics in Africa with James OtienoSummary In this episode of the Bioinformatics Lab podcast, James Oteno shares his journey as a bioinformatician and genomic epidemiologist, discussing the intersection of bioinformatics and public health, particularly in the context of emerging pathogens in Africa. The conversation covers the importance of both wet lab and dry lab skills, the role of KEMRI in global health, and the impact of COVID-19 on public health practices. Oteno also delves into the MPOX outbreak, the rapid sequencing technology used in Ebola outbreaks, and the future of genomic epidemiology in Africa, emphasizing the need for collaborative networks and equitable partnerships in global...
2025-09-191h 00the bioinformatics lab
the bioinformatics labEP 60: NGS for Veterinary Diagnostics with Janina Krumbeck (MiDog)In this episode of the Bioinformatics Lab Podcast, Janina Krumbeck shares her unique journey from Germany to the United States, detailing her academic experiences and the challenges she faced during her PhD program. She discusses the importance of mentorship, the transition from academia to industry, and her current role in the microbiomics team at Zymo Research. Janina emphasizes the value of persistence and finding a fulfilling career path in the biotech industry.
2025-08-2149 minthe bioinformatics lab
the bioinformatics labEP 59: Navigating Bioinformatics and Public Health with Amy GaskinIn this conversation, Amy Gaskin shares her journey into bioinformatics, detailing her transition from an ecological background to a career in public health. She discusses the pivotal moments that led her to discover her passion for bioinformatics, the essential skills she acquired during her master's program, and her experiences working in pathogen genomics during the COVID-19 pandemic. Amy emphasizes the importance of workflow management, containerization, and standardization in bioinformatics, particularly in the context of public health. She also reflects on her current work modernizing HIV pipelines and the collaborative efforts within the field.
2025-08-0459 minthe bioinformatics lab
the bioinformatics labEP 58: From Veterinary Medicine to Pathogen Genomics with Gültekin ÜnalIn this episode of the Bioinformatics Lab podcast, Gültekin Ünal shares his unique journey from veterinary medicine to bioinformatics, highlighting the pivotal moments that shaped his career. For more information about the PHA4GE organization discussed in this episode, please visit: https://pha4ge.org/ He discusses the importance of microbiology in understanding diseases, the impact of COVID-19 on public health practices, and the significance of the One Health approach in integrating animal and human health. Gültekin emphasizes the role of bioinformatics in pathogen surveillance and the need for collaboration within the scientific community to address global health cha...
2025-07-211h 21the bioinformatics lab
the bioinformatics labEP 57: Open Conversation with Tommy TangTommy's Blog: https://divingintogeneticsandgenomics.com/ Summary In this conversation, Kevin Libuit and Tommy Tang explore the journey of communication in science, particularly in the field of bioinformatics. They discuss the importance of sharing knowledge, the transition from wet lab to computational biology, and the evolution of bioinformatics tools. Tommy shares his experiences with learning Unix, the balance between remote work and in-person interactions, and the mindset of finding opportunities in crises. The conversation highlights the significance of humility, continuous learning, and the interconnectedness of roles within the scientific community. Takeaways Tommy started his blog to document his learning journey in...
2025-06-2749 minthe bioinformatics lab
the bioinformatics labEP 53: Remote WorkSummary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss the evolution of remote bioinformatics work, exploring the benefits and challenges of remote work, the importance of in-person interactions, and the ongoing debate surrounding the return to office policies. They share personal experiences and insights on how remote work has transformed their professional lives, the impact of commuting on quality of life, and the necessity of fostering communication and connection in a virtual environment. Takeaways Remote work allows hiring the best talent globally. Quality of life improves with reduced commuting time. In-person interactions enhance team...
2025-05-0211 minthe bioinformatics lab
the bioinformatics labEP 51: Software BugsSummary In this episode, Kevin Libuit and Andrew Page discuss the complexities of software bugs, focusing on the distinction between user errors and software errors. They explore the importance of understanding user needs and the challenges of software compatibility, particularly in the context of bioinformatics. The conversation emphasizes the need for a multidisciplinary approach to software development and troubleshooting. Takeaways A lot of software lacks proper engineering and testing. User errors often stem from simple mistakes like formatting. Debugging requires careful attention to detail. New line endings can cause compatibility issues across systems. User documentation is crucial for effective troubleshooting. ...
2025-04-0213 minthe bioinformatics lab
the bioinformatics labEP 52: Genomic Epidemiology with Krisandra AllenSummary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Krisandra Allen discuss the integration of bioinformatics and epidemiology, focusing on the challenges and solutions in utilizing genomic sequencing data for infectious disease surveillance. They explore the roles of epidemiologists and bioinformaticians, the importance of communication and collaboration, and the need for bi-directional learning to enhance public health practices. The conversation emphasizes the significance of building relationships and understanding each other's fields to effectively turn sequencing data into actionable insights for disease control. Takeaways Epidemiologists work on the front lines of public health. Genomic data can help build...
2025-04-0134 minLife Science Success
Life Science SuccessInside the Gene Code: Bioinformatics Revealed with Dr. EdwardsSend us a textIn this episode of the Life Science Success Podcast my guest is Michael Edwards, the founder and CEO of Bioinfo Solutions LLC, a data analytics company specializing in extracting insights from complex biological information. Dr. Edwards brings over two decades of experience in genomics, spanning from laboratory research to teaching data science and bioinformatics, with a passion for deciphering the genetic language of cells.00:00 Introduction to Life Science Success Podcast00:38 Sponsor Message: Bio on the Bayou 202502:12 Guest Introduction: Michael Edwards02:36 Michael's Journey...
2025-03-2852 minthe bioinformatics lab
the bioinformatics labEP 50: Software NamingSummary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss the art and challenges of naming bioinformatics tools. They explore various naming conventions, the significance of unique and memorable names, and the creative strategies employed by developers. The conversation also touches on the importance of trademark considerations and the potential pitfalls of naming conflicts in the bioinformatics community. Takeaways Naming bioinformatics tools is crucial for usability. A good name should be unique and memorable. Backronyms are a common naming strategy. Consistency in naming is important for software development. Names can be inspired by personal experiences...
2025-03-0310 minSustainable Winegrowing
Sustainable Winegrowing263: Make Better Wines with BioinformaticsTiny microbes have a big impact on wine quality. Aria Hahn, CEO and co-founder of Koonkie, Inc., discusses the exciting work her bioinformatics organization is doing in the field of metagenomics. Hahn explains the differences between genetics, genomics, and metagenomics. She shares insights from a project studying yeast populations in British Columbia's Okanagan region, revealing the diversity and distinct clades found on wine grapes. The conversation also covers the broader applications of bioinformatics in agriculture, including regenerative farming, soil health, and potential bioprotectants against wine spoilage. Hahn underscores the impact of microbiome management on wine terroir and the potential...
2025-02-2041 minthe bioinformatics lab
the bioinformatics labEP 49: H5N1 OutbreakSummary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the ongoing H5N1 outbreak, its implications for public health, and the economic impact on agriculture. They explore the nature of avian influenza, the risks of mammalian spillover, and the importance of genomic surveillance in understanding and combating the virus. The conversation highlights the rapid advancements in vaccine development and the need for ongoing monitoring to prevent future outbreaks. Takeaways H5N1 is a highly pathogenic avian influenza affecting poultry and cattle. Influenza viruses are adept at recombining, posing pandemic risks. The current H5N1...
2025-02-1317 minthe bioinformatics lab
the bioinformatics labEP 48: The Kalamari DatabaseKalamari GitHub: https://github.com/lskatz/Kalamari & Public Health Announcement: https://journals.asm.org/doi/10.1128/mra.00963-24 Summary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss a public health announcement regarding the Kalamari database, a curated reference database for public health pathogenomics. They explore the importance of high-quality genomic data, the implications of mobile genetic elements, and the various applications of the database in public health. The conversation highlights the collaborative efforts of experts in the field and the significance of reliable data in making informed public health decisions. Takeaways The Kalamari database is...
2025-02-0214 minthe bioinformatics lab
the bioinformatics labEP 47: The Job Hunt Experience pt. 02Summary In this episode of the Buy Informatics Lab podcast, Kevin Libuit and Andrew Page discuss the intricacies of the job market from a recruiter's perspective. They share insights on how to effectively navigate the recruitment process, the importance of leveraging professional networks, and the role of online platforms like LinkedIn and GitHub in identifying and attracting talent. The conversation emphasizes the significance of having a strong digital footprint and the strategies that can help candidates stand out in a competitive job market. Takeaways Successful hires often come from personal networks. Recommendations from trusted colleagues add value. Passion for bioinformatics...
2025-02-0215 minthe bioinformatics lab
the bioinformatics labEp. 46: The Job Hunt Experience pt. 01Summary In this episode, Kevin Libuit and Andrew Page discuss their personal experiences with job hunting in the bioinformatics field, emphasizing the importance of professional networks and genuine relationships. They share anecdotes about how their careers were shaped by connections made through academia and social interactions. The conversation highlights actionable advice for job seekers, including leveraging social media and engaging with the community to build a robust professional network. Takeaways All jobs can stem from knowing the right people. Building a professional network is essential for career growth. Genuine curiosity and kindness can lead to unexpected opportunities. Networking should be...
2025-01-0116 minMicro binfie podcast
Micro binfie podcast133 The Role of Bioinformatics in Public Health and Disease OutbreaksIn 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...
2024-12-0512 minthe bioinformatics lab
the bioinformatics labEp 46: TheiaGenEpiTheiaGenEpi is now freely accessible at https://theiagenepi.org/ Summary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss TheiaGenEPI, a significant project under the Theiagen Global Health Initiative (TGHI). They explore the transition of the CZ GenEPI tool to TGHI, highlighting the technical challenges and solutions involved in this process. The conversation delves into the software engineering aspects of bioinformatics, emphasizing the importance of user experience and cloud services in modern genomic epidemiology. The episode concludes with a look at the future of phylogenetic analysis, particularly in relation to SARS-CoV-2 and monkeypox. Takeaways TheiaGenEPI...
2024-12-0411 minthe bioinformatics lab
the bioinformatics labEp 45: Pathogen Focus - MPXVSummary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the complexities of analyzing MPXV genomes, particularly in light of recent outbreaks. They explore the differences between MPXV and other viruses, the challenges faced in genomic sequencing and analysis, and the importance of public health responses, including vaccination efforts. The conversation highlights the need for updated tools and resources to effectively monitor and respond to MPXV outbreaks globally. Takeaways Viruses require different types of treatment and analysis. MPXV is a larger virus compared to SARS-CoV-2. Amplicon dropout is a significant concern in sequencing. Public health...
2024-11-2109 minMicro binfie podcast
Micro binfie podcast131 Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global GenomicsIn 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 Ch...
2024-11-0712 minRoleCatcher.com : Interviews Uncovered
RoleCatcher.com : Interviews UncoveredBioinformatics Scientist : Job Interviews UncoveredMastering the Bioinformatics Scientist Interview: Essential Questions and Expert TipsAre you gearing up for a bioinformatics job interview and feeling uncertain about what lies ahead? In this episode of RoleCatcher Job Interviews Uncovered, we delve into the specific interview questions you can expect while pursuing a career as a bioinformatics scientist and share essential tips to help you shine. From analyzing complex biological data to creating innovative algorithms, bioinformatics scientists play a pivotal role in advancing healthcare and life sciences. Excelling in the interview process is a key step toward securing your desired position...
2024-10-2927 minthe bioinformatics lab
the bioinformatics labEp 44: Career Focus:Julian Paganini & Olinto Linares-PerdomoNote: This episode was recorded in Spanish. A video of this recording with AI-generated, English subtitles is available on YouTube: https://www.youtube.com/watch?v=FNjUbtcm9Z4 Summary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit hosts Julian and Olinto in a special Spanish-language episode. They discuss their journeys in bioinformatics, the importance of collaboration in science, and their experiences at a hackathon. The conversation highlights the barriers of language in accessing scientific resources and the significance of community in learning and sharing knowledge. Takeaways The podcast aims to provide resources in Spanish for the scientific community. ...
2024-10-2825 minMicro binfie podcast
Micro binfie podcast129 Genomics on the Frontier: Bactopia, Bioinformatics, and Pathogen Surveillance with Robert PetitHost 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...
2024-10-1114 minthe bioinformatics lab
the bioinformatics labEp 43: Pathogen Focus: Dengue VirusSummary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the challenges and limitations in analyzing dengue virus genomes using bioinformatics. They highlight the importance of open-source tools, the need for better data sharing, and the complexities of virus typing compared to bacteria. The conversation emphasizes the neglected status of dengue as a pathogen and the urgent need for improved methodologies in public health. Takeaways Dengue is a small but significant virus affecting warmer climates. Current mathematical tools for dengue analysis are inadequate. Open-source tools are essential for sustainable dengue typing. Phylogenetic placement is crucial...
2024-10-1111 minthe bioinformatics lab
the bioinformatics labEp 42: GMI 14, Barcelona, SpainSummary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss their experiences at the GMI 14 conference in Barcelona, reflecting on the importance of metadata in microbial bioinformatics, the role of AI in data sharing, and the significance of communicating the 'why' behind bioinformatics initiatives. They explore differing opinions on metadata's importance, the implications of AI technology, and the need for sustainable practices in the field. Takeaways GMI 14 maintained the spirit of GMI 13 with a focused cohort. The importance of metadata in tracking outbreaks was debated. AI's role in microbial bioinformatics is growing. Rich metadata enhances...
2024-09-2310 minthe bioinformatics lab
the bioinformatics labEp 41 Importance of Dev EnvironmentsSummary In this episode, Kevin and Andrew discuss the importance of dev environments in bioinformatics and the adoption of software engineering practices. They highlight the need for separate environments for development, production, and staging, and the importance of stability and consistency in production code. They also emphasize the role of testing and automated processes in ensuring code quality. The conversation touches on the maturation of the field and the need for standardized practices in bioinformatics. They conclude by discussing the impact of bioinformatics on real-life decisions and the importance of professionalism in the field. Takeaways Dev environments are separate environments...
2024-09-0316 minthe bioinformatics lab
the bioinformatics labEp 40 Career Spotlight: Sharvari NarendraSummary In this conversation, Sharvari Narendra shares her career journey in bioinformatics, which includes experiences in academia, industry, and a startup. She emphasizes the importance of exploring different career tracks and finding alignment with personal passions. Sharvari highlights the creativity and problem-solving skills required in bioinformatics, as well as the need to understand the tools and pipelines used in data analysis. She also discusses the differences between working in academia and industry, including flexibility and the level of collaboration. Sharvari encourages early career professionals to attend conferences, network, and continue learning in order to advance in the field.
2024-08-0242 minthe bioinformatics lab
the bioinformatics labEp 40: GenEpi Platform MigrationSummary In this episode, Kevin Libuit and Andrew Page discuss the life cycle of different platforms in the software and public health bioinformatics space. They talk about the CZ GenEoi platform, which is now migrating to the TheiaGenEpi moniker as part of the Theiagen Global Health Initiative. They highlight the importance of providing resources to low and middle-income countries (LMICs) and the challenges of transitioning and maintaining a software project. They also discuss the impressive engineering behind the GenEpi platform, including its use of cloud components, scalability, and orchestration with Terraform. The conversation emphasizes the collaborative nature of the public...
2024-07-2615 minthe bioinformatics lab
the bioinformatics labEp 39: Bioinformatics HackathonsASM NGS Hackathon Details: - Date: 10-12 October 2024 - Location: Washington DC, Venue TBD (within 30 minutes of the ASM NGS venue) - Registration form: https://lnkd.in/e8KTqZYQ - Admission: Free (Sponsored by Theiagen Genomics) Summary In this episode, Kevin and Andrew discuss hackathons and the upcoming ASM NGS Hackathon. They explain that hackathons bring together people from different backgrounds to work on community problems and solve common challenges. The hackathon at ASM NGS will be a virtual and in-person event, allowing for broader participation. They emphasize the value of community building and networking that comes from hackathons, as...
2024-07-1214 minthe bioinformatics lab
the bioinformatics labEp 38: Workflow InfrastructureAlso available on YouTube: https://youtu.be/i9oT5ku11is Summary In this episode, Kevin and Andrew discuss different mechanisms to run and support bioinformatics pipelines. They explore the use of workflows, workflow managers, and graphic user interfaces for pipeline execution. They highlight popular workflow options such as Nextflow, Terra, and Galaxy, and discuss the benefits of using standardized workflow languages. They also emphasize the importance of scalability and the drawbacks of creating in-house pipeline systems. The conversation concludes with a discussion on the differences in data models and administrative overhead among the different workflow options. Takeaways Understanding workflows...
2024-06-2718 minthe bioinformatics lab
the bioinformatics labEp 36: Technical Career TracksAlso available on YouTube: https://youtu.be/ZlKYKuOeGZc Summary In this episode, Kevin Libuit and Andrew Page discuss the different levels of a bioinformatics developer and the career track in the field. They explain that bioinformatics is a relatively new field and the levels have emerged over time. The entry-level position is called a junior or associate bioinformatics scientist, where individuals follow established protocols and apply existing tools. The senior level involves more independent work and ownership of bioinformatics solutions. The principal level focuses on strategic decision-making and technical leadership. The hosts emphasize the importance of finding happiness and fulfillment...
2024-05-2217 minthe bioinformatics lab
the bioinformatics labEp 35: Bioinformatics in the CloudSummary In this episode, Kevin and Andrew discuss cloud computing in the context of bioinformatics. They explore the different layers of cloud technology and how it can be implemented in laboratories. They highlight the benefits of cloud computing, such as quick access to resources, cost savings, and scalability. They also discuss the challenges of managing costs and ensuring security in a cloud environment. Overall, they emphasize the importance of understanding the specific needs of bioinformatics and choosing the right cloud infrastructure. Takeaways Cloud computing offers quick access to resources and cost savings compared to on-premises infrastructure. The specific needs of...
2024-05-0819 minde-CIPHERing Infectious Disease
de-CIPHERing Infectious DiseaseBioinformatics with Dr. Dan JaniesEpisode 2 In this episode, we are joined by co-director of CIPHER and bioinformatics expert: Dr. Dan Janies. He discusses his background and work in using computational methods and genomic data to study infectious diseases. He explains how he traced the origins of the SARS coronavirus to bats and used bioinformatics to track the spread of diseases like SARS, bird flu, and COVID-19 variants. Dr. Janies describes innovating techniques like projecting phylogenetic trees onto Google Earth to visualize disease movement and calculating protein structures to predict immune evasion. He shares his vision for "functional molecular epidemiology" to not just detect...
2024-05-071h 03the bioinformatics lab
the bioinformatics labEp 33: Communicating Results in Public HealthSummary In this episode, Kevin Libuit and Andrew Page discuss the challenges of communicating complex genomic information to different audiences in public health. They explore the need for tailored communication strategies for various stakeholders, including bioinformatics scientists, epidemiologists, and the general public. The power of analogies in simplifying complex concepts is highlighted, along with the importance of building bridges between different technical fields. The conversation also emphasizes the need to communicate the limits and nuances of genomic data, and the role of genetic relatedness as a proxy for epidemiological associations. Overall, the episode underscores the ongoing need for effective communication...
2024-04-0814 minthe bioinformatics lab
the bioinformatics labEp 32: Best Practices - Pipeline Development, Part ThreeSummary This episode of the Bioinformatics Lab Podcast continues the conversation on public health pipeline best practices. The focus is on pipeline functionality, documentation for local install and remote access, and example usage. The hosts discuss the importance of clearly articulating the function of a pipeline and the different pipeline systems available. They emphasize the need for documentation that includes instructions for installation and usage, as well as providing example data. The episode concludes with a call to read the best practices document and the announcement of future efforts to promote and assess adherence to these practices. Takeaways Clearly articulate...
2024-04-0115 minthe bioinformatics lab
the bioinformatics labEp 32: Best Practices - Pipeline Development, Part TwoPHA4GE Ten Best Practices for Public Health Bioinformatics Pipelines: https://github.com/pha4ge/public-health-pipeline-best-practices/blob/main/docs/pipeline-best-practices.md Summary In this episode, Kevin Libuit and Andrew Page discuss the 10 best practices for public health pipeline development. They start by emphasizing the use of common file formats and the importance of avoiding reinventing the wheel. They highlight the benefits of standard file formats and the availability of parsers for different languages. They also discuss the implementation of software testing, including the use of automated testing and the integration of testing with Docker containers. They emphasize the need for...
2024-03-2316 minthe bioinformatics lab
the bioinformatics labEp 32: Best Practices - Pipeline Development, Part OnePHA4GE Ten Best Practices for Public Health Bioinformatics Pipelines: https://github.com/pha4ge/public-health-pipeline-best-practices/blob/main/docs/pipeline-best-practices.md Summary In this episode, Andrew Page and Kevin Libuit discuss best practices for public health bioinformatics pipelines. They highlight the importance of code availability, open source licensing, version control, workflow management systems, and containerized and packaged software. These practices aim to improve transparency, reproducibility, and interoperability in the field of bioinformatics. Takeaways Code availability and open source licensing are crucial for transparency and collaboration in public health bioinformatics. Version control allows for the tracking of software changes and facilitates...
2024-03-1618 minthe bioinformatics lab
the bioinformatics labEp29 Career Spotlight: Kevin G. LibuitIn this episode, Kevin Libuit discusses his career in the world of public health, pathogen genomics, and bioinformatics. He shares his journey from studying biology with the intention of pursuing a medical career to discovering his passion for bioinformatics during his undergraduate research. Kevin explains how he transitioned from medicine to bioinformatics and joined the Virginia State Lab, where he became involved in national initiatives and the creation of the State Public Health Bioinformatics Working Group (StaPH-B). He also talks about his time at Theiagen and the ever-evolving nature of bioinformatics careers. Takeaways Bioinformatics careers often involve unconventional paths and...
2024-02-2223 minthe bioinformatics lab
the bioinformatics labEp28 Food Safety Research NetworkSummary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the Food Safety Research Network and a recent conference they attended. The network brings together government, academia, and industry to focus on food safety research. The conference had an interactive format, encouraging networking and collaboration among participants. The network provides funding for research projects and aims to bridge the gap between academia and industry. The conference covered various topics, including the influence of social media on food safety and challenges with new cooking devices and novel foods. The future steps for the Food Safety Research...
2024-02-1617 minthe bioinformatics lab
the bioinformatics labEp 25 Containerized SoftwareEp 25 Containerized Software by The Bioinformatics Lab
2024-01-2619 minthe bioinformatics lab
the bioinformatics labEp 24 Reasons to (or not to) Pursue a PhDEp 24 Reasons to (or not to) Pursue a PhD by The Bioinformatics Lab
2024-01-2218 minthe bioinformatics lab
the bioinformatics labEp 23 Benefits of Cloud Computing for BioinformaticsIn this episode we discuss the shift from traditional High-Performance Computing (HPC) systems to cloud computing in bioinformatics. Key points of the conversation include: Transition to Cloud Computing: The discussion begins with the gradual adoption of cloud computing over the past 5-6 years in bioinformatics, highlighting that for many scientists, moving from an HPC infrastructure to the cloud represents a significant change. Experiences with HPC and Cloud Transition: Andrew shares his experience transitioning from a traditional HPC setup to a cloud system, describing the process and the initial challenges faced, such as adapting to different software and operational methods. Benefits...
2024-01-1215 minthe bioinformatics lab
the bioinformatics labEp 22 Bridging Bytes and Biology: The Dynamics of Team-Based Bioinformatics Software DevelopmentThe discussion centers around the dynamics of bioinformatics software development and contrasts it with academic settings. Key points include: Transition from Solo to Team Development: The podcast delves into the shift from working individually in an academic setting, where a developer might handle everything on a personal computer, to contributing to a larger codebase in a team environment. This transition involves learning how to collaborate effectively, manage code reviews, and adapt to different software development practices. Professional Growth and Open Source Projects: Kevin shares his experiences from James Madison University and the Virginia Public Health Laboratory, highlighting his journey from...
2024-01-0716 minthe bioinformatics lab
the bioinformatics labEp 21 Science and Social Media🔊 Welcome to another insightful episode of The Bioinformatics Lab Podcast! Join us as we delve into the dynamic world of social media and its impact on the scientific community. 📢 In this episode: Kevin shares his journey from a Twitter lurker to an active participant in the scientific Twitterverse. Andrew discusses the evolution of academic communication, from traditional journals to the rapid-fire world of social media. The duo explores the balance between being a consumer and a producer of scientific content online. They tackle the challenges and opportunities presented by various platforms, including Twitter, LinkedIn, and emerging spaces like Blue Sky and Ma...
2023-12-2915 minthe bioinformatics lab
the bioinformatics labEp 20 Contextual Data StandardsEp 20 Contextual Data Standards by The Bioinformatics Lab
2023-12-2315 minthe bioinformatics lab
the bioinformatics labEp 19 Foodborne PathogensJoin us as we dive into the fascinating world of next-generation sequencing (NGS) and bioinformatics in the surveillance of foodborne pathogens. Our discussion covers the evolution of foodborne pathogen surveillance, from traditional methods to modern advancements like NGS. We examine the challenges posed by new business models like dark kitchens and home-based food businesses, and the implications for food safety in light of changing consumer trends and complex supply chains. The conversation shifts to the technological leaps in public health laboratories, particularly the transition from methods like Pulse Field Gel Electrophoresis to Whole Genome Sequencing. Kevin and Andrew discuss the...
2023-12-1616 minthe bioinformatics lab
the bioinformatics labEp 18 Responding to Emerging Public Health ThreatsIn this episode of The Bioinformatics Lab podcast, we delve into the critical topic of public health responses to emerging infectious diseases. This discussion is particularly relevant in the post-COVID-19 era, where the importance of public health has been brought to the forefront of global awareness. 🔬 Key Highlights Evolving Nature of Infectious Diseases: A focus on the recent surge in mycoplasma pneumoniae infections and the complexities involved in tracking and naming new strains. From the Lab to the Frontlines: Insights into the laboratory and bioinformatics side of responding to infectious disease outbreaks. Public Health’s Strategy: An in-depth look at the a...
2023-12-0816 minthe bioinformatics lab
the bioinformatics labEp 17 MetagenomicsJoin us in this enlightening episode of the Bioinformatics Lab podcast, where we dive deep into the world of metagenomics. In this episode, we explore the complexities and challenges of metagenomics, both from a wet lab and bioinformatics perspective, offering insights into this rapidly evolving field. 🔬 *Key Topics Covered:* 1. *Understanding Metagenomics:* An introduction to the field, highlighting its complexities compared to traditional microbiological techniques. 2. *Techniques in Focus:* Differentiating between amplicon-based sequencing and shotgun metagenomics, and their unique applications. 3. *Navigating Technical Challenges:* Discussing the difficulties in assembling and analyzing diverse DNA mixtures from environmental samples. 4. *Public Health Implications:* Exploring the shift in...
2023-12-0216 minthe bioinformatics lab
the bioinformatics labEp 16 Bioinformatics ConferencesKevin and Andrew discuss major bioinformatics conferences coming up in 2024, including: ABPHM (Applied Bioinformatics and Public Health Microbiology) - Held every 2 years in the UK, next one likely in 2025. Smaller size (~150 people), very applied and focused on implementation. ASM NGS (ASM Next Generation Sequencing Conference) - US equivalent of ABPHM, also applied and implementation focused. Next one is in October 2024. PHA4GE (Public Health Alliance for Genomic Epidemiology) - Large conference focused on genomic epidemiology. Held every 2 years, next location TBD. They also briefly touch on some mega conferences like ASM Microbe and ISMB, but note they tend to prefer...
2023-11-2416 minthe bioinformatics lab
the bioinformatics labEp 15 Campylobacter genomics and epidemiologyDr Ozan Gundogdu from The London School of Hygiene and Tropical Medicine (LSHTM) and Dr Arnoud van Vliet from the University of Surrey join Andrew to chat about Campylobacter genomics and epidemiology. This was recorded at LSHTM. This episode of the Bioinformatics Lab podcast discusses Campylobacter genomics and epidemiology. Campylobacter is a major cause of foodborne illness, with over 200,000 cases annually in the UK traced mainly to poultry. While genomic databases hold a wealth of Campylobacter sequences, undiscovered diversity likely remains. Research shows connections between virulence factors and sequence types, aiding epidemiological inference. In the UK, poultry and cattle are...
2023-11-1619 minthe bioinformatics lab
the bioinformatics labEp 14 The first PHA4GE conference: Harmonizing Efforts in Genomic SurveillanceIn this episode, Kevin shares his experiences and key takeaways from the first PHA4Ge conference which has just been held in South Africa, focusing on genomic surveillance and pathogen genomics. Kevin discusses the central theme of the conference: establishing and agreeing upon quality assurance standards for genomic surveillance. The need for unified standards across laboratories and countries is emphasized, as the current practice often leads to inconsistent approaches and results. The speaker notes that there has been progress in establishing quality control metrics for certain pathogens, such as SARS-CoV-2, through initiatives like PulseNet. However, there is acknowledgment that more...
2023-11-1016 minthe bioinformatics lab
the bioinformatics labEp 13 PHA4GE: The Public Health Alliance for Genomic EpidemiologyIn this episode, we delve deep into PHA4GE, the Public Health Alliance for Genomic Epidemiology. Join us as we explore the nuances of establishing universal metadata standards and the powerful impact of international collaboration. 🎙️ What to Expect: PHA4GE: Global leadership in public health genomics. Contextual Metadata Standards: Discover how the meticulous establishment of metadata standards has revolutionized genomic data sharing and research. SARS-CoV-2 Sequencing Journey: Take a journey through the complexities and breakthroughs in sequencing the most studied pathogen in history. Unprecedented Global Unity: Learn about the awe-inspiring international cooperation between labs and research institutions during the pandemic. Leade...
2023-11-0315 minthe bioinformatics lab
the bioinformatics labEp 11 Genomics informed pandemic policyIn this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page delve deep into the significant impacts of COG-UK during the COVID-19 pandemic. Highlighting a groundbreaking paper by Dr Dinesh Aggarwal from the University of Cambridge, they discuss the role of genomic data in assessing quarantine measures to prevent the importation and spread of SARS-CoV-2. Discover how genomics painted a clearer picture of new virus lineages entering the UK and how these insights influenced government policies. Dr Aggarwal won the Royal College of Pathologists (RCPath) Silver Research Medal for this work. Join us as we explore the fusion...
2023-10-1715 minthe bioinformatics lab
the bioinformatics labEp 10 COG-UK: Pioneering SARS-CoV-2 Sequencing during the PandemicIn this episode of the Bioinformatics Lab podcast, hosted by Kevin Libuit and Andrew Page from Theiagen, the primary focus is on COG-UK. COG-UK stands out as a premier consortium for SARS-CoV-2 sequencing and set the benchmark for many international groups during the COVID-19 pandemic, especially in the realms of sequencing, analysis, and reporting. Andrew Page, having played a pivotal role in COG-UK, sheds light on its inception, objectives, and background. Contrary to its grand impression, COG-UK was majorly formed by professionals already acquainted with each other from the UK genomics arena. By March 2020, there was a pressing demand to...
2023-10-1016 minthe bioinformatics lab
the bioinformatics labEp 9 Update from Global Microbial IdentifierThe podcast, set against the picturesque backdrop of Vancouver, delves into the intricate world of bioinformatics, emphasizing the pivotal role of the Global Microbial Identifier (GMI) in facilitating discussions on data sharing, public health, and international collaborations. Organizers Emma and Will, along with other professionals underscore the challenges in data sharing due to varied international laws, privacy concerns, and technical roadblocks. A significant highlight was the discourse on the importance of respecting the data rights of indigenous and marginalized communities, particularly the First Nations, and the ethical considerations surrounding it. Moreover, the collaboration with Lebanon on SARS-CoV-2 research exemplified the...
2023-10-0513 minthe bioinformatics lab
the bioinformatics labEp 7 Technological Advancements in public health bioinformaticsHosted by Kevin Libuit and Andrew Page, the podcast focuses on the evolution of tech adoption in pathogen genomics. The narrative begins with the shift from traditional software packages to modern cloud-based GUIs. Early software installations were cumbersome, often taking weeks and requiring an in-depth understanding of dependencies and compilers. There was also a notable shift in programming languages from Ruby and Perl to Python. Package managers evolved from systems like Debian and Homebrew to Conda and BioConda, with Mamba offering further installation improvements. The podcast touched on the use of Make as an early workflow manager and its evolution...
2023-09-2025 minthe bioinformatics lab
the bioinformatics labEp 6 Regional Differences in Public HealthHosts Kevin Libuit and Andrew Page discuss public health bioinformatics. - They delve into the regional differences in the implementation of bioinformatics in public health, comparing the U.S. and the U.K. - Kevin shares his experience from the Virginia State Public Health Sciences. In 2016, public health labs in the U.S. began transitioning from traditional techniques to whole genome sequencing. - Kevin was one of the first bioinformatics scientists in Virginia and was part of a small group of state-level bioinformatics scientists. - Challenges faced by states in bioinformatics implementation weren't always easily addressed by federal bodies like...
2023-09-1319 minthe bioinformatics lab
the bioinformatics labEp5 Public Health PerspectiveKevin Libuit began his career in public health bioinformatics in Virginia, USA, while Andrew Page's experience mainly leans towards the academic side. Differences between Academia and Public Health: - Academia is flexible, allows for experimentation, and tends to focus on niche, blue-sky research. - Public health emphasizes quality, validation, reproducibility, and the impact on real-world actions, such as informing government responses or legal actions related to health concerns. Tool Development and Use: - Academia often reinvents tools, leading to many solutions for the same problem. - Public health focuses on the implementation and consistent use of tools for actionable insights. ...
2023-09-0919 minthe bioinformatics lab
the bioinformatics labEp4 AI starter kit for BioinformaticiansIn this episode of The Bioinformatics Lab podcast, hosts Kevin and Andrew discuss how bioinformaticians can get started with integrating AI into their workflows. They begin by recommending signing up for ChatGPT on OpenAI as the very first step. ChatGPT provides a chatbot interface to access the GPT models, allowing users to have conversations and get text responses. Paying for a premium account gives access to GPT-4, the most advanced chatbot model. An alternative free option is Anthropic's Claude. With access to ChatGPT or Claude, some starter ways bioinformaticians can make use of it are asking it to explain bioinformatics...
2023-08-2227 minthe bioinformatics lab
the bioinformatics labEp3 Will we be replaced by AI robots?The hosts Kevin and Andrew discuss whether bioinformaticians will be replaced by AI and robots. They note how AI is already being used to generate synthetic voices, images, and video of people, threatening industries like voice acting and extras. Bioinformatics is a complex field requiring creative problem-solving, so full automation seems far off. AI will likely play an assistive role to bioinformaticians. AI may reduce the number of bioinformaticians needed due to increased productivity, but demand for the skillset is very high.The role of bioinformaticians will evolve as tasks become more automated, requiring adaptation to new technologies. Ethical issues...
2023-08-1520 minthe bioinformatics lab
the bioinformatics labEp2 Getting started with AI in bioinformaticsIn this episode of the Bioinformatics Lab podcast, hosts Kevin Libuit and Andrew Page discuss the intricacies of implementing AI technologies in bioinformatics laboratories. They express excitement about AI's potential but caution that understanding its implementation and limitations is essential. The hosts draw analogies and provide examples to illustrate the out-of-the-box readiness of AI technologies like GPT. They emphasize the importance of enthusiasm and expert champions to drive the technology forward in the field while also highlighting potential pitfalls, such as AI-generated misinformation and "hallucinations." They explore concerns about AI being influenced by biased or incorrect data and the importance...
2023-08-0825 minthe bioinformatics lab
the bioinformatics labEp 1 A new world of Large Language Models for bioinformaticsThe Bioinformatics Lab podcast, hosted by Kevin Libuit and Andrew Page, begins with an exploration of Large Language Models (LLMs), like ChatGPT. The hosts underscore the ubiquity and growing influence of these models in today's world, noting their rising awareness among the global adult population. They delve into the realm of bioinformatics, discussing the transformative potential of LLMs in this space. They elucidate how these models can process and interpret vast datasets, a task crucial in modern biology. They further delve into the specifics of genomic sequence interpretation, highlighting how LLMs can aid in deciphering the complex language of genes...
2023-07-2647 minMicro binfie podcast
Micro binfie podcast110 ChatGPT: The Bioinformatics CalculatorIn 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...
2023-07-0626 minMicro binfie podcast
Micro binfie podcast109 AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial BioinformaticsIn this episode of the Micro Binfie Podcast, titled "AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics", Lee, Nabil, and Andrew unpack the implications of generative predictive text AI tools, notably GPT, on microbial bioinformatics. They kick off the conversation by outlining the various applications of AI tools in their work, which range from generating boilerplate programs, drafting documents, to summarizing vast tracts of data. Andrew talks about his experience with GPT in coding, specifically via VS Code and GitHub Copilot, highlighting how GPT can generate nearly 90% of the necessary code based on a brief description...
2023-06-2230 minMicro binfie podcast
Micro binfie podcast99 Stories from the frontlines of bioinformaticsAt the 8th Microbial Bioinformatics Hackathon in Bath we talked to a live panel with Kristy Horan, Torsten Seemann, Finlay Maguire and Andrew Page about bioinformatics from the frontlines. We apologise for the poor audio quality, it was recorded in a room with 20 people in the background so at points it got a bit loud, however we felt you might enjoy the discussion regardless.
2023-01-2639 minMicro binfie podcast
Micro binfie podcast98 Nomadic bioinformatics with FrankWe interview Frank Ambrosio. He is embarking on a lifestyle of nomadic bioinformatics, living his best life. * https://www.linkedin.com/in/francis-ambrosio/ In this episode of the MicroBinfie podcast, Frank Ambrosio, a bioinformatician working for Theiagen as a traveling bioinformatician, joins co-hosts Andrew Nabil and Lee to talk about his journey into bioinformatics. Frank shares how he transitioned from being a lab technician and microbiologist to analyzing his own data and pursuing a master's program in bioinformatics at Georgia Tech. He also discusses his experience working at the CDC, where he gained exposure to different laboratories working on tuberculosis...
2023-01-1242 minInside Matters
Inside MattersEpisode 003 - Dr Morgan Langille – microbiome bioinformatics, DNA sequencing, metagenomicsDr Morgan Langille, an expert in bioinformatics, talks about developing novel technologies and techniques that enable a better understanding of human-microbial interactions.    Dr Langille discusses advances in the microbiome field as well as combining computer science and microbiology to lead to new therapeutics and diagnostics.   Episode Time Stamps 00:00 Intro 00:30, How Dr Langille got into the field of the microbiome 04:30, Gene duplication and reverse transcription 05:48, What is bioinformatics? 06:34, The evolution of bioinformatics  09:30, Genomic islands 1:04 - Phages 14:30 Dr Langille’s first bioinformatics tool  16:00 Bacterial genome libraries  18:20 Extremeophilic bacteria 19:00 Will there be bugs in space 21:42 Bacteria on Mars  22:15 Human microbiome diversity  23:30 Number of human cell...
2022-10-201h 48Micro binfie podcast
Micro binfie podcast90 Public health bioinformatics on the cloud with WDL + Terra.bio90 Public health bioinformatics on the cloud with WDL + Terra.bio by Microbial Bioinformatics
2022-09-2944 minMicro binfie podcast
Micro binfie podcast89 What do we do with WDL?Today on the @microbinfie podcast, we talk about WDL with @sevinsky and @DannyJPark. We learn what widdle means to Andrew and his kids. Joel takes a shot at Lyve-SET and you'll never guess what happens next. In the MicroBinfie podcast, we discuss the workflow description language (WDL) commonly used to describe bioinformatics pipelines in a portable and cross-environmental way. The starting point is the presumption that tools are already containerized, and WDL helps to bind them together. The guests highlighted that this standardizes bioinformatics in the field, making it more reproducible and scalable. It also helps remove the need for...
2022-09-1526 minThe Thor Hour
The Thor HourMiranda Darby - Bioinformatics - Episode #6 - The Thor HourMiranda Darby is assistant professor of bioinformatics at Hood College.  Miranda has a Ph.D. in molecular biology and genetics from the Johns Hopkins School of Medicine.  She has a passion for studying the human genome and teaching others to do the same.   Her current research focuses on the development of computational methods to identify and quantify the expression of novel RNAs using whole genome RNA sequencing. Join us in this conversation as Miranda speaks bout the challenges and possibilities that bioinformatics holds for us. EPISODE LINKS: Miranda Darby - https://www.hood.edu/academics/fac...
2022-07-081h 44Micro binfie podcast
Micro binfie podcast85 Breaking the dogma with bioinformaticsWe are joined again by Prof Mark Pallen who takes us through his early experiences in high-throughput microbial genomics. Mark was pleased that he persuaded Nick Loman to join him in Birmingham. Mark tells us how they worked with George Weinstock to perform the first genome sequence analyses of Gram-negatives for genomic epidemiology—in this case of multi-drug resistant Acinetobacter baumannii. After winning an Ion Torrent sequencer in a competition, Mark and Nick then contributed some pioneering genomic analyses of the German STEC outbreak. One of their studies involved crowd sourced approaches, primed by Twitter and was published in the Ne...
2022-06-2327 minMicro binfie podcast
Micro binfie podcast84 Bioinformatics in the noughties with Mark PallenMark Pallen explains how exciting it was to be in microbial bioinformatics around the turn of the millennium, as we gained genomes for the first time from model organisms and fearsome pathogens. He recounts working with his hero David Relman on the genome sequencing of the strange slow-growing organism called Tropheryma whipplei in competition with a French team. Mark moved to Belfast in late 1999 collaborating with another Englishman working on the island of Ireland, Tim Foster in Dublin. Pallen describes the addictive exhilaration of using PSI-BLAST to find new sortases and sortase substrates across a range of new genomes—for hi...
2022-06-0922 minFuture Science Group
Future Science GroupTech Blast | Sculpting bioinformatics workflows for NGS data analysisIn this episode, supported by Zymo Research, guest host Georgia Bickerton explores NGS data and how bioinformatic pipelines and workflows can be optimized to make NGS data more accessible. To do this she speaks with Jeffrey Bhasin, Director of Informatics at Zymo Research, who discusses the key issues of reproducibility in bioinformatics, the selection of methods available to analyze different datasets and to investigate different aspects of these data. Listen today to discover the techniques available to help increase the portability and reproducibility of fine-tuned bioinformatics workflows and to streamline the application of these workflows. Bhasin also reveals how these...
2022-06-0815 minMicro binfie podcast
Micro binfie podcast82 Bioinformatics moments before the millenniumIn this episode we talk to Professor Mark Pallen, who discusses the highlights from his long career as a medical microbiologist turned bioinformatician. His bioinformatics journey began in 1977, the year Fred Sanger invented DNA sequencing-as-we know-it, when Mark was tasked with assembling some amino acid sequences under exam conditions. Mark explains how little was know about sequences at the time. Luckily he managed to gain a grasp of molecular biology and joined a group in the late 1908s at Barts Hospital in London, where he met Brendan Wren. Mark's first eureka moment followed shortly afterwards, when he analysed sequences encoding...
2022-05-1239 minMicro binfie podcast
Micro binfie podcast79 StaPH-B: Stable containers for public health bioinformaticsDr Erin Young from the Utah Department of Health and Dr Kelsey Florek from the Wisconsin State Laboratory of Hygiene join us to talk about StaPH-B containers for public health bioinformatics. Its basically how to make biology easier for everyone! Github: https://github.com/StaPH-B
2022-04-1428 minMicro binfie podcast
Micro binfie podcast78 StaPH-B: state public health bioinformaticsDr. Erin Young and Dr Kelsey Florek join us to talk about StaPH-B, a US state public health bioinformatics group. They also give some insights into the popular SARS-CoV-2 pipeline cecret. Website: staphb.org/ Cecret Pipeline: github.com/CDCgov/SC2CLIA Kelsey explains that StaPH-B was created to facilitate collaborations between bioinformaticians in state public health laboratories, especially those just getting started with sequencing and understanding the data generated. The organization provides a conduit of communication and expertise among different laboratories, feeding into projects funded by the NIH, CDC, and other grant agencies. Erin highlights StaPH-B's diverse membership with different...
2022-03-3125 minProgress, Potential, and Possibilities Podcast / Show
Progress, Potential, and Possibilities Podcast / ShowDr. Lamya Abdulaziz AlOmair, Ph.D. - Head of A.I. and Bioinformatics - KAIMRC (Saudi Arabia)Send us a textDr. Lamya Abdulaziz AlOmair, Ph.D. is the Head of Artificial Intelligence (A.I.) and Bioinformatics, at King Abdullah International Medical Research Center (https://kaimrc.ksau-hs.edu.sa/), and an affiliated faculty member in the systems biology group at George Mason University. Dr. AlOmair is one of the first Saudi women to obtain a Bachelor Degree in Computer Science, from King Saud University, following which she joined the Saudi National Guard Health Affairs (NGHA) initially as a Programmer and Database Specialist, and was later promoted to Database Administrator and Manager of Human Resource...
2022-02-2631 minMicro binfie podcast
Micro binfie podcast73 Bactopia and using workflow managers in bioinformatics part 2We are again joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20
2022-01-2028 minMicro binfie podcast
Micro binfie podcast72 Bactopia and using workflow managers in bioinformatics part 1We are joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20
2022-01-0635 minMicro binfie podcast
Micro binfie podcast75 How to review a bioinformatics paper in 10 days or lessWe discuss how to effectively review bioinformatics papers, what to look out for and tips for researchers to when writing bioinformatics or microbial genomics papers to ease their way through review.
2021-11-0231 minData Engineering Podcast
Data Engineering PodcastAn Exploration Of The Data Engineering Requirements For BioinformaticsSummary Biology has been gaining a lot of attention in recent years, even before the pandemic. As an outgrowth of that popularity, a new field has grown up that pairs statistics and compuational analysis with scientific research, namely bioinformatics. This brings with it a unique set of challenges for data collection, data management, and analytical capabilities. In this episode Jillian Rowe shares her experience of working in the field and supporting teams of scientists and analysts with the data infrastructure that they need to get their work done. This is a fascinating exploration of the collaboration between...
2021-09-1955 minBJSM Podcast
BJSM PodcastWhat should you keep track of? Bioinformatics for Female Athletes with Dr. Dusty Narducci. Ep #460On this week’s podcast, Dr. Dusty Marie Narducci, MD speaks with Dr. Ben Krainin, MD on the AMSSM Sports Medcast about the use of bioinformatics and wearable technology in female athletes. In this conversation, Dr. Narducci focuses the following topics: · A general overview of bioinformatics, including the three main wearable technology product categories · Injury Prevention in Volleyball Players · Menstrual Tracking for Female Athletes · Fitness Trackers for the “General Consumer” This lecture features multiple key points and takeaways about bioinformatics and was originally scheduled to be presented during the 2020 AMSSM Annual Meeting.
2021-01-1521 minMicro binfie podcast
Micro binfie podcast37 Ontologies - the secret sauce of bioinformaticsDr Emma Griffiths and Dr João Carriço join us to give us a crash course on ontologies, the bioinformatics secret sauce that makes all things work well. Microbial genomics data is like the Tower of Babel with public health talking to food regulators talking to agriculture talking to veterinarians talking to healthcare, all with different languages to describe similar things. So how do we get any work done at all? Listen in to why you need ontologies in your life!
2020-12-2424 minThe Bioinformatics and Beyond Podcast
The Bioinformatics and Beyond PodcastDr. Todd Treangen: Fall 2020 Bioinformatics RoundupDr. Todd Treangen gives us an update on what's been going on lately in the field of bioinformatics. We begin with a discussion on the best ways to stay current in bioinformatics. Dr. Treangen discusses the roles of the wide variety of sources of information such as conferences and journals. In particular, he expands on the role of social media sites like twitter in science. Finally, Dr. Treangen covers some of the current bioinformatics buzz, such as the integration of machine learning and the progress on a final, fully finished human genome sequence.
2020-10-2448 minThe Bioinformatics and Beyond Podcast
The Bioinformatics and Beyond PodcastDr. Luay Nakhleh: What is Bioinformatics?What is Bioinformatics? What is the Bioinformatics and Beyond Podcast? What is the difference between Bioinformatics and Computational Biology? What skill sets are required to become a Bioinformatician? How would someone take their first step into the world of Bioinformatics? What career options are out there for Bioinformaticians?
2020-09-2630 minMicro binfie podcast
Micro binfie podcast25 Sustainable bioinformatics softwareHow do you make bioinformatics software sustainable so that we can move our field from academic research into hospitals and doctors offices? We discuss the nuts and bolts of making sustainable bioinformatics software and changes you can make in your own practices: Documentation, Coding styles, Versioning, SOPs and capturing institutional knowledge, Software licencing, Automated testing, Measuring your impact, and going the commercial route.
2020-07-3027 minTheOpenShow | Tech for Everyone
TheOpenShow | Tech for EveryoneEpisode 8: Quantum Computing, Bioinformatics and Big DataIn this week’s episode, Aarav Makadia discusses the importance of quantum computing and the emergence of bioinformatics and big data. With the global emergence of data, the power efficiency of quantum computing makes it more promising than modern computing. Bioinformatics works to bring the intersection of biology and computer science in order to develop software tools in order to generate useful biological information. Big Data works to analyze extremely large datasets to reveal patterns, trends, and associations to human behavior. How will quantum computing change the way we interact with computers? Where will bioinformatics be used? How are gl...
2020-07-1728 minAcadHelp Talks
AcadHelp TalksIntroduction to Bioinformatics Part 2In this episode discussion is on Introduction to Bioinformatics. Ms. Ajanta Panda, PGT (Biotech), KV No. 1 Sambalpur (Odisha) is the guest speaker today. This discussion will clarify the doubts of students on this topic and will get answers to their unanswered questions. The following were discussed 1. Where is actually these databases are deposited so that they can be accessed Worldwide at the time of need ? 2. Explain in detail about  Biological  databases that are frequently used in Bioinformatics & also highlight their utility in Biological Sciences .
2020-05-2632 minAcadHelp Talks
AcadHelp TalksIntroduction to Bioinformatics Part 1In this episode discussion is on Introduction to Bioinformatics. Ms. Ajanta Panda, PGT (Biotech), KV No. 1 Sambalpur (Odisha) is the guest speaker today. This discussion will clarify the doubts of students on this topic and will get answers to their unanswered questions. The following were discussed 1. What is Bioinformatics?  2.What are the prime objectives of Bioinformatics?  3. Why is the term "Dry Lab" used for defining Bioinformatics  ? 4. Give a brief account of Historical perspectives of Bioinformatics.  5.Why do we...
2020-05-2626 minData Futurology - Leadership And Strategy in Artificial Intelligence, Machine Learning, Data Science
Data Futurology - Leadership And Strategy in Artificial Intelligence, Machine Learning, Data Science#109 Programming, Bioinformatics and the Future of Computer Programming with Ken Youens-Clark – Senior Scientific ProgrammerKen is a senior-level programmer with over 23 years of experience developing software in industry and research environments. Ken is a self-taught computer programmer, software engineer, hacker and teacher. What started off as developing websites in the early 90’s turned into an extensive and fruitful career in bioinformatics and eventually teaching and mentorship. Ken is also the author of Tiny Python Projects published by Manning Publications. Enjoy the show! We speak about: [00:30] About Ken Youens Clark [02:00] Ken’s Work and COVID-19 [03:15] How did you get into the bioinformatics field? [13:00] Ken’...
2020-05-1254 min