the bioinformatics lab

Summary 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 responses can effectively contain outbreaks. Genomic surveillance is crucial for monitoring MPXV. Different variants of MPXV require updated reference genomes. Vaccination efforts can limit the spread of M-Pox. The availability of hosts affects the outbreak dynamics. Bioinformatics tools need to be adaptable for different viruses. Collaboration among international labs enhances genomic analysis.

Note: 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. Julian's journey began in Argentina, focusing on bioinformatics and data fusion. Olento's background includes mathematical modeling and pharmacokinetics. Collaboration is key in scientific research and development. Hackathons provide excellent opportunities for networking and learning. Cultural exchange enriches the scientific community. Free online resources like Coursera are valuable for learning. The importance of community in overcoming learning barriers. Experiences at hackathons can lead to significant collaborations. Creating resources in Spanish is essential for inclusivity in science.

Summary 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 for understanding circulating strains. Different countries have unique circulating dengue types. Amplicon sequencing is a viable method for dengue analysis. Data sharing in the viral world is significantly limited. The viral taxonomy system is less organized than that of bacteria. There is a pressing need for better tools and methods for dengue research. The conversation around dengue needs to be expanded and prioritized.

Summary 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 genomic epidemiology applications. Data sharing can lower the burden of collaboration. The 'why' behind bioinformatics initiatives is crucial for sustainability. Case studies can illustrate the impact of bioinformatics. Melbourne is set to host GMI 15 next year. Engaging with policymakers is essential for funding. The conference fosters connections among key players in the field.

Summary 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 for development, production, and staging, and are essential for mitigating risks and ensuring code stability. Testing and automated processes play a crucial role in maintaining code quality and confidence in production code. The field of bioinformatics is maturing, and the adoption of software engineering practices and standardized practices is necessary for the widespread use of bioinformatics technologies. Bioinformatics has real-life impacts and requires professionalism to ensure the accuracy and reliability of the data. In the applied space, curiosity and drive for continuous improvement should be focused on solving the problems faced by the user base.

Summary 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.

ASM 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 well as the opportunity to collaborate and work on specific projects. They encourage people to bring their curiosity and willingness to collaborate to hackathons, regardless of their technical background. Takeaways Hackathons bring together people from different backgrounds to work on community problems and solve common challenges. The ASM NGS Hackathon will be a virtual and in-person event, allowing for broader participation. Hackathons provide opportunities for community building, networking, and collaboration. Participants should bring their curiosity and willingness to collaborate, regardless of their technical background.

Also 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 is a fundamental skill in bioinformatics. Popular workflow options include Nextflow, Terra, and Galaxy. Standardized workflow languages help standardize development and execution. Using out-of-the-box solutions reduces the need for creating in-house pipeline systems. Consider the data model and administrative overhead when choosing a workflow option.

YouTube: https://youtu.be/RybtspKHkgA Summary The conversation discusses the topic of SRA Lite, a data storage format for genomic information. SRA Lite is a compressed version of the original data, with the quality scores removed. The conversation highlights the challenges and controversies surrounding SRA Lite, including the loss of data granularity and the confusion around accessing the original files. The lack of clear communication from NCBI is also mentioned as a problem. The conversation suggests that the normalized files should be the default format for user access and retrieval. Overall, better communication and understanding of SRA Lite are needed. Takeaways SRA Lite is a compressed version of genomic data that removes quality scores. The use of SRA Lite has sparked controversy due to the loss of data granularity. There is confusion around accessing the original files and distinguishing between SRA Lite and full FASTQ files. Better communication and understanding of SRA Lite are needed to address user frustrations.

Also 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 at any level in the field. Takeaways Bioinformatics is a relatively new field, and the levels of a bioinformatics developer have emerged over time. The entry-level position involves following established protocols and applying existing tools. The senior level requires more independent work and ownership of bioinformatics solutions. The principal level focuses on strategic decision-making and technical leadership. It is important to find happiness and fulfillment at any level in the field.

Summary 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 bioinformatics, such as high volume and different hardware requirements, should be considered when setting up a cloud infrastructure. Managing costs and ensuring security are important challenges in a cloud environment. Cloud computing provides scalability and flexibility to meet the evolving needs of bioinformatics.

PHA4GE Website: https://pha4ge.org/ Summary Alan Christoffels, the principal investigator for the Public Health Alliance for Genomic Epidemiology (PHA4GE), discusses the challenges and future directions of the consortium. He shares his background as a scientist and director of a program leading international collaborations in pathogen genomics. The conversation highlights the importance of global community building and the need to connect laboratories across borders to address common challenges in public health. The impact of PHA4GE in the response to the COVID-19 pandemic is also discussed, along with the value of creating a community of practice and providing opportunities for professionals to contribute. Alan invites individuals from various backgrounds to get involved in PHA4GE and contribute to its mission. Takeaways PHA4GE is a global consortium that aims to connect laboratories across borders to address common challenges in public health. Alan Christoffels emphasizes the importance of global community building and the need to involve individuals from various backgrounds in PHA4GE. The impact of PHA4GE in the response to the COVID-19 pandemic is discussed, highlighting the value of creating a community of practice and providing opportunities for professionals to contribute. Alan encourages individuals to get involved in PHA4GE and contribute to its mission.

Summary 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 in the field of genomics and public health. Takeaways Tailored communication strategies are necessary when communicating complex genomic information to different audiences in public health. Analogies can be powerful tools for simplifying complex concepts and making them relatable to a wide range of stakeholders. Building bridges between different technical fields, such as bioinformatics and epidemiology, is crucial for effective communication. Communicating the limits and nuances of genomic data is essential to avoid misinterpretation and ensure proper understanding.

Summary 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 the function of a pipeline in the field of public health bioinformatics. Use pipeline systems like Galaxy and Terra to visually represent and manage workflows. Provide clear documentation for local installation and remote access of pipelines. Include example usage and data to facilitate understanding and testing of pipelines.

PHA4GE 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 accessibility to benchmark or validation data sets and the importance of reference data requirements. They also touch on the significance of hiring bioinformaticians and the documentation practices that should be followed. Takeaways Use common file formats to avoid reinventing the wheel and enable compatibility with other programs. Implement software testing, including automated testing, to ensure functionality and identify bugs. Provide benchmark or validation data sets to allow users to compare and evaluate the performance of the pipeline. Consider the reference data requirements and ensure accessibility to curated databases. Hire bioinformaticians with domain expertise to navigate the complexities of pipeline development. Follow documentation practices, including communication of authorship, pipeline maintenance statements, and community guidelines for contribution and support.

PHA4GE 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 collaboration. Workflow management systems provide standardization and interoperability in pipeline development. Containerized and packaged software ensures reproducibility and simplifies software installation.

Summary In this episode, Kevin Libuit and Andrew Page discuss the use of AI-generated images in scientific publications. They start by addressing a recent retracted publication that featured images with anatomical inaccuracies and AI-generated labels. They highlight the failure of the peer review process and the responsibility of reviewers, editors, and authors in detecting such issues. The conversation expands to the broader problem of data manipulation and the potential use of AI in scientific writing. They also discuss the need for quality over quantity in publishing and the future of peer review. Takeaways The use of AI-generated images in scientific publications can lead to inaccuracies and fraudulent representations. The peer review process failed to detect the issues in the retracted publication, highlighting the need for improved review practices. AI has the potential to assist in scientific writing, but caution must be exercised to ensure accuracy and transparency. The publishing industry needs to prioritize quality over quantity and address the problem of low-quality journals accepting subpar papers.

Manuscript Discussed: https://www.science.org/doi/10.1126/sciadv.adi0497 Summary This conversation discusses a study that explores the relationship between the gut microbiome and cognitive function. The study design involved collecting stool samples and cognitive function scores from a diverse population of children. The researchers used various statistical methods, including linear models and machine learning, to analyze the data. The results showed associations between specific microbial profiles and cognitive function scores, as well as correlations with brain regions. The study suggests the potential for using the gut microbiome as a screening tool and for future interventions to improve cognitive development. Takeaways The gut microbiome may play a role in cognitive development and function. Specific microbial profiles are associated with cognitive function scores. Machine learning techniques can help identify important microbial features. The gut microbiome may have implications for brain regions and cognitive performance.

Manuscript Discussed: https://www.science.org/doi/10.1126/sciadv.adi0497 Summary In this episode, Dr. Kevin Bonham discusses the relationship between the gut microbiome and brain development. He explains the concept of the gut-brain axis and provides evidence for the connection between the two. Dr. Bonham also highlights the mutability of the gut microbiome and its potential impact on cognitive outcomes. The main objective of the study is to explore the association between gut microbiome profiles and cognitive capabilities in healthy individuals. Takeaways The gut microbiome and brain development are connected through the gut-brain axis. The gut microbiome plays a role in cognitive outcomes, including neurodevelopment and mental health. The gut microbiome is mutable and can be influenced by factors such as diet and antibiotics. Understanding the relationship between the gut microbiome and brain development can lead to potential interventions for cognitive impairments.

In 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 opportunities that arise along the way. Transitioning from one field to another requires making difficult decisions and following your passion. Collaboration and communication among bioinformatics scientists at the state and national levels are crucial for addressing common challenges. The field of bioinformatics is constantly evolving, and new positions and opportunities are being created.