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Artificial intelligence is rapidly becoming part of how we write, research, organize information, apply for jobs, clean data, learn new skills, and build professional workflows. But as these tools become more powerful, another question becomes increasingly important: how can we use AI in a way that is practical, transparent, and more respectful of user control?This is where d’BiYOK Lab begins.d’BiYOK Lab is a parallel project space within PagBiOmicS, created to explore practical AI-assisted tools beyond the strictly bioinformatics and omics context. While PagBiOmicS remains connected to biodiscovery, scientific training, omics, and applied research, d’BiYOK Lab expands that mindset toward broader productivity applications.<figure id="figure-adal0p637ymrcbptl6" data-full-width=""><img id="adal0p637ymrcbptl6" src="https://cdn.durable.co/blocks/19Z1vNWHsWDLr5kdTz3yM2J5K8Eybc12oxSfLLCdBCzgaXbVilBSKzrOyoJM7GSu.png" alt="" title="" class="object-cover bg-gray-100 " style="aspect-ratio: 16/9; object-position: 10% 60%;" data-corners="no-rounded" data-aspect="16:9" data-caption="" data-positionx="10%" data-positiony="60%" data-fullwidth="true" data-mce-src="https://cdn.durable.co/blocks/19Z1vNWHsWDLr5kdTz3yM2J5K8Eybc12oxSfLLCdBCzgaXbVilBSKzrOyoJM7GSu.png" data-mce-style="aspect-ratio: 16/9; object-position: 10% 60%;"></figure>The idea is simple: build focused tools that help people work better with AI, while making the process easier to understand.What d’BiYOK MeansThe name d’BiYOK combines two ideas.Bi reflects a Biodiscovery-Integrated perspective: the PagBiOmicS habit of connecting science, data, workflows, and applied problem-solving.BYOK means Bring Your Own Key. In this context, it refers to applications where users can connect their own AI provider API key, such as Gemini, OpenAI, Claude, DeepSeek, GLM, Ollama, or other compatible systems.Together, d’BiYOK Lab represents a space for AI-assisted applications that are practical, transparent, educational, and user-oriented.<h3>Why Create a Parallel Space?</h3>PagBiOmicS started from a scientific and bioinformatics-oriented foundation. But many of the same principles that make scientific workflows useful also apply to broader productivity:<ul><li>structure messy information,</li><li>make outputs editable,</li><li>keep workflows reproducible,</li><li>help users understand what the tool is doing,</li><li>reduce unnecessary dependence on opaque platforms,</li><li>and treat AI as an assistant, not as a black box.</li></ul>d’BiYOK Lab allows PagBiOmicS to explore these ideas in a wider setting.The goal is not only to build tools for researchers. The goal is to support professionals, students, entrepreneurs, educators, job seekers, and everyday users who want practical AI workflows without losing control of their documents, keys, or process.<h3>A Practical Educational Layer</h3>d’BiYOK Lab is not only about releasing tools. It is also about helping users understand AI infrastructure in simple terms.Many people use AI daily without knowing what an API key is, where their data goes, what a model provider can see, or why local execution may be better for some workflows.Each d’BiYOK app should therefore help answer practical questions:<ul><li>What is being sent to the AI model?</li><li>Which provider is being used?</li><li>Where are files stored?</li><li>Can I use my own API key?</li><li>Can I run part of the workflow locally?</li><li>How can I export and keep control of my outputs?</li><li>How should I handle browser-entered API keys safely?</li></ul>This educational layer is part of the project.<h3>Beyond Research: Wider Productivity Applications</h3>Although the project grows naturally from PagBiOmicS, d’BiYOK Lab is not limited to bioinformatics or academic research.The same approach can support many types of practical tools:<ul><li>literature and document assistants,</li><li>data cleaning utilities,</li><li>job application workflows,</li><li>business planning helpers,</li><li>learning and training apps,</li><li>writing and editing tools,</li><li>local knowledge-base assistants,</li><li>small automation tools for professionals and citizens</li></ul><h3>Closing Perspective</h3>d’BiYOK Lab is a parallel PagBiOmicS space for exploring practical AI-assisted productivity tools.It is experimental, but intentional !!!

d’BiYOK Lab: A Parallel PagBiOmicS Space for Practical AI-Assisted Productivity Tools

<h3>✨ Conus Snails and Conotoxins</h3>Marine gastropods, commonly known as cone snails (Conus genus), produce a sophisticated mixture of venomous peptides called conopeptides. These peptides are remarkable for their potent and highly specific action on ion channels, receptors, and transporters within the nervous system. This specificity positions conopeptides as valuable resources for physiological studies of neuroreceptors and promising leads for drug development. The structural diversity of conotoxins, coupled with the rapid evolution of their gene superfamilies, enhances their significance in evolutionary biology.<figure id="figure-1zjq973gambs3beg7"><img id="1zjq973gambs3beg7" src="https://cdn.durable.co/blocks/38LafBxNFgkWtE5vXLIXiQgElKmq0AnF29LeBIlLyOHJMrKD0XIlS6uxjg6Upsls.png" alt="Shell Collection" title="Shell Collection" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 3/2; object-position: 45% 35%;" data-corners="default" data-aspect="3:2" data-caption="" data-positionx="45%" data-positiony="35%" data-fullwidth="false" data-mce-src="https://cdn.durable.co/blocks/38LafBxNFgkWtE5vXLIXiQgElKmq0AnF29LeBIlLyOHJMrKD0XIlS6uxjg6Upsls.png" data-mce-style="aspect-ratio: 3/2; object-position: 45% 35%;"></figure>With over 700 Conus species worldwide, each potentially producing up to 200 distinct peptides, the number of conopeptides discovered to date is in the thousands. Many more remain to be characterized. This diversity supports research into the co-evolution of venom repertoires and their molecular targets. Additionally, conopeptides are commonly used in neurophysiology to probe receptor isoforms, leveraging the evolutionary conservation of ion channels and receptors.Conopeptides are classified into two broad categories:<ul><li>Disulfide-rich conotoxins (two or more disulfide bonds)</li><li>Disulfide-poor peptides (one or no disulfide bond)</li></ul>These peptides are typically 10–40 amino acids long. Within ConoServer, classification relies on three schemes:<ul><li>Pharmacological families (based on target specificity)</li><li>Gene superfamilies (signal peptide sequence similarity)</li><li>Cysteine frameworks (bonding pattern in the mature region)</li></ul>🎯 Pharmacological Targets: Diversity and SignificanceConotoxins are notable for their high specificity and potency in modulating both voltage-gated and ligand-gated ion channels in neurological and muscular systems.Examples of pharmacological families:<ul><li>μ-, μO-, and δ-conotoxins: Target voltage-gated Na⁺ channels by various mechanisms.</li><li>ω-conotoxins: Block voltage-gated Ca²⁺ channels. ω-Conotoxin MVIIA is the active component in Prialt (ziconotide), a non-opioid drug for chronic pain.</li><li>κ- and κM-conotoxins: Target K⁺ channels.</li><li>α-conotoxins: Antagonists of nicotinic acetylcholine receptors (nAChRs).</li><li>χ-conotoxins: Block the neuronal noradrenaline transporter.</li><li>ρ-conotoxins: Act on α1-adrenoceptors.</li><li>σ-conotoxins: Target serotonin-gated 5-HT3 ion channels.</li><li>ι-conotoxins: Modulate Na⁺ channels without delayed inactivation.</li><li>γ-conotoxins: Affect neuronal pacemaker cation currents.</li><li>τ-conotoxins: Interact with somatostatin receptors.</li></ul><figure id="figure-s7jam3o8jlmbtdbw5m"><img id="s7jam3o8jlmbtdbw5m" src="https://cdn.durable.co/blocks/21o3wGH5E1Xqq500a3rwbl4NFcCYTccQx2XdEgUcQ36O1tHOc27DOa8QfonKyIyP.png" alt="" title="" class="object-cover bg-gray-100 rounded-2xl md:rounded-3xl lg:rounded-4xl" style="aspect-ratio: 3/2; object-position: undefined undefined;" data-corners="large" data-aspect="3:2" data-caption="" data-positionX="undefined" data-positionY="undefined" data-fullWidth="false"/></figure><a data-mce-href="https://www.conoserver.org/index.php" href="https://www.conoserver.org/index.php">ConoServer</a> is a curated database of conopeptide sequences and structures, maintained by the Institute for Molecular Bioscience (IMB), Australia. Created in 2007, it is maintained by researchers including David Craik, Jan-Christoph Westermann and Quentin Kaas (Kaas et al., 2008; 2012).Data sources include peer-reviewed publications and databases like UniProtKB, NCBI Nucleotide, and PDB. Manual curation ensures:<ul><li>Sequence analysis and annotation</li><li>Identification of gene superfamilies and cysteine frameworks</li><li>Mapping of mature peptides</li><li>Recording of post-translational modifications</li></ul><figure id="figure-pjva81yhigmbtdkvsj"><img id="pjva81yhigmbtdkvsj" src="https://cdn.durable.co/blocks/5w18kSjGd4QSMtIphLVf0mKa0PsysyWGTCqhT2IggGAgNxTxvpW55p4D24gIf2RI.png" alt="" title="" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 3/2; object-position: center center;" data-corners="small" data-aspect="3:2" data-caption="" data-positionx="undefined" data-positiony="undefined" data-fullwidth="false" data-mce-src="https://cdn.durable.co/blocks/5w18kSjGd4QSMtIphLVf0mKa0PsysyWGTCqhT2IggGAgNxTxvpW55p4D24gIf2RI.png" data-mce-style="aspect-ratio: 3/2; object-position: center center;"></figure>Key Features:<ul><li>Multi-criteria search: Based on taxonomy, classification, geography, and sequence.</li><li>Detailed entry cards: Cover protein, nucleotide, and structural data.</li><li>Statistical reports: Automatically updated data on species, structures, classifications, and citations.</li><li>Precursor sequence tools: ORF prediction, region detection, homolog search.</li><li>Mass spectrometry tools: PTM prediction and mass list analysis.</li></ul>🔍 Identified Inconsistencies and Data Issues in ConoServerDespite the comprehensive resources provided by ConoServer, practical limitations in data handling and interoperability can emerge during routine research workflows. These challenges often hinder the seamless transition from raw database information to advanced analysis.Specific Challenges Encountered:1. &nbsp; &nbsp; Inconsistent FASTA Data Handling: Retrieving sequences from ConoServer often presents difficulties with FASTA formatting. Direct copying and pasting of sequences and headers into text files or other tools can introduce "unknown characters" or misinterpret the critical &gt; symbol, essential for FASTA header recognition. This issue complicates the process of obtaining clean, bulk FASTA files ready for downstream computational analysis.2. &nbsp; &nbsp; Workflow Bottleneck with Downstream Prediction Tools: A significant challenge involved using ConoServer-derived sequence data with external bioinformatics tools, such as ConoPrec, for predicting mature peptides. Even with meticulously cleaned FASTA files, these prediction tools frequently failed to process multi-sequence inputs, often only recognizing and analyzing the first sequence in a given file. Besides, there is no option to save the resulting mature peptides in a FASTA file, so this limitation necessitates time-consuming, manual, one-by-one processing for large datasets, or additional scripting skills to populate the sequences from the tabular format.<h3>💡 ConoServerParser: Complementary Conotoxin FASTA Analysis Suite for ConoServer DATA</h3>Although ConoServer is comprehensive, limitations remain when preparing data for downstream workflows. <a data-mce-href="https://danysaurio.shinyapps.io/ConoServerParser/" href="https://danysaurio.shinyapps.io/ConoServerParser/">ConoServerParser</a>, a Shiny application, was developed to enhance the analyses of the data exported from ConoServer. Despite the comprehensive resources provided by ConoServer, practical limitations in data handling and interoperability can emerge during routine research workflows. These challenges often hinder the seamless transition from raw database information to advanced analysis.<figure id="figure-3mmuzcip85mbtckzr8"><img id="3mmuzcip85mbtckzr8" src="https://cdn.durable.co/blocks/12QXVy2aKUZoTYHDhPDjmZKnWQPoILHr8X5sCrTLjOL0WEVtJLzoRqGsMEBxjBcT.png" alt="" title="" class="object-cover bg-gray-100 rounded-2xl md:rounded-3xl lg:rounded-4xl" style="aspect-ratio: 1/1; object-position: undefined undefined;" data-corners="large" data-aspect="1:1" data-caption="" data-positionx="undefined" data-positiony="undefined" data-fullwidth="false" data-mce-src="https://cdn.durable.co/blocks/12QXVy2aKUZoTYHDhPDjmZKnWQPoILHr8X5sCrTLjOL0WEVtJLzoRqGsMEBxjBcT.png" data-mce-style="aspect-ratio: 1/1; object-position: undefined undefined;"></figure>Common Challenges Resolved:FASTA formatting issues: Pasting sequences may introduce encoding errors (e.g., broken headers). Complex filtering: Lack of intuitive filtering tools and insufficient metadata in exported headers. Batch tool compatibility: Tools like ConoPrec often fail to process multiple sequences at once.<h3>ConoServerParser Features:</h3><figure id="figure-herdlpsbmbtf7t18"><iframe id="herdlpsbmbtf7t18" src="https://www.youtube.com/embed/ZgRrB305xRg" class="w-full bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9;" allowfullscreen="" data-url="https://youtu.be/ZgRrB305xRg" data-corners="default" data-fullwidth="false" data-mce-src="https://www.youtube.com/embed/ZgRrB305xRg" data-mce-style="aspect-ratio: 16/9;"></iframe></figure>• FASTA parsing and intelligent metadata extraction: Reliably interprets ConoServer’s pipe-delimited headers, automatically parsing fields like ConoID, species, gene superfamily, pharmacological family, cysteine framework, and evidence level into a clean tabular format. • FASTA export customization: Offers configurable FASTA header generation with user-selected fields and custom delimiters, supporting fine-tuned downstream integration. • Multi-format data export: Export sequence metadata tables as CSV, TSV, or XLSX; or generate downloadable ZIP archives grouped by metadata (e.g., superfamily or pharmacological family). • Mature peptide FASTA generation: Automatically extract and format mature sequences from ConoPrec CSV output, eliminating ConoPrec’s multi-sequence limitations. • Advanced filtering and interactive interface: Select, filter, and exclude entries across multiple fields using an intuitive sidebar with dropdowns and search tools. • Dynamic visual summaries: Create interactive bar plots to compare sequence distributions across superfamilies, pharmacological families, or evidence types. • Header preview and export configuration: Preview how final FASTA headers will look, control included metadata, and avoid oversized headers or unnecessary fields. • Custom FASTA export: Filtered or grouped downloads with customizable headers. • ZIP archive generation: Organize exports by superfamily or pharmacological category. • Mature peptide FASTA generation: Upload CSV output from ConoPrec to obtain well-formatted mature sequences. • Interactive filtering: Flexible filter UI for any column. • Data visualization: Generate plotly bar charts of sequence distributions. • Multi-format exports: Download tables in TSV, CSV, XLSX. 🧾 SummaryConoServer offers an invaluable foundation for conopeptide research. ConoServerParser extends this utility, addressing real-world bottlenecks in data handling and exploration. Together, these tools enhance the efficiency and reproducibility of workflows in pharmacology, evolutionary biology, and peptide synthesis.📚 ReferencesKaas Q, Yu R, Jin AH, Dutertre S, Craik DJ. (2012). ConoServer: updated content, knowledge, and discovery tools in the conopeptide database. Nucleic Acids Research, 40(Database issue): D325–D330. Kaas Q, Westermann JC, Halai R, Wang CK, Craik DJ. (2008). ConoServer, a database for conopeptide sequences and structures. Bioinformatics, 24(3): 445–446. ConoServer. Accessed May 20, 2025. https://www.conoserver.org/ Intrathecal Pain Management. (2023). In Pain Management: Anesthesia, Analgesia, and Opioid Alternatives. &nbsp;

🧪 ConoServerParser: A Flexible Shiny Application for Filtering, Exploring, and Exporting Conotoxin Sequences from ConoServer

<a data-mce-href="https://academic.oup.com/bioinformaticsadvances/article/5/1/vbae183/7905457" href="https://academic.oup.com/bioinformaticsadvances/article/5/1/vbae183/7905457">SeqLengthPlot</a> is a simple yet powerful tool designed to help researchers analyze, visualize, and extract sequence length information from FASTA files. Originally developed as a <a data-mce-href="https://github.com/danydguezperez/SeqLengthPlot" href="https://github.com/danydguezperez/SeqLengthPlot">Python CLI tool</a>, it allows users to split sequences by a length threshold, generate customizable distribution plots, and obtain detailed statistics.We’ve now expanded this functionality with an interactive <a data-mce-href="https://github.com/danydguezperez/SeqLengthPlot/tree/main/SeqLengthPlot.shiny" href="https://github.com/danydguezperez/SeqLengthPlot/tree/main/SeqLengthPlot.shiny">R Shiny app version</a>! <a data-mce-href="https://danysaurio.shinyapps.io/seqlengthplot/" href="https://danysaurio.shinyapps.io/seqlengthplot/">Accessible directly from your browser</a>, this new interface maintains all the original functionalities while adding the convenience of interactivity — no coding required.<figure id="figure-3v0b2fxyf5m9vo7ge5"><img id="3v0b2fxyf5m9vo7ge5" src="https://cdn.durable.co/blocks/32iK2FPrkDlK4IeXqmVhPAQUAMvrlGGKTUHHHepPR9FhdWOnmjTclRn1XkTtIREq.png" alt="" title="" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9; object-position: center center;" data-corners="default" data-aspect="16:9" data-caption="" data-positionx="undefined" data-positiony="undefined" data-fullwidth="false" data-mce-src="https://cdn.durable.co/blocks/32iK2FPrkDlK4IeXqmVhPAQUAMvrlGGKTUHHHepPR9FhdWOnmjTclRn1XkTtIREq.png" data-mce-style="aspect-ratio: 16/9; object-position: center center;"></figure> 🧪 What’s new in the Shiny version? • Easily upload your DNA or protein FASTA files • Set a length cutoff and automatically split sequences above or below this threshold • Instantly visualize the length distribution (linear and log scale) • Customize plot colors and export figures (PDF, PNG, SVG) • Download split FASTA files and summary statistics<figure id="figure-0z7j4321slem9vn8st8"><iframe id="0z7j4321slem9vn8st8" src="https://www.youtube.com/embed/iE3NXettRmM" class="w-full bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9;" allowfullscreen="" data-url="https://youtu.be/iE3NXettRmM?si=3i57qmm0lQXDYmGp" data-corners="default" data-fullwidth="false" data-mce-src="https://www.youtube.com/embed/iE3NXettRmM" data-mce-style="aspect-ratio: 16/9;"></iframe></figure>🎥 As you might be interested in trying it, we’ve also created a comprehensive <a data-mce-href="https://youtu.be/iE3NXettRmM?si=3i57qmm0lQXDYmGp" href="https://youtu.be/iE3NXettRmM?si=3i57qmm0lQXDYmGp">▶️ video tutorial</a> showing how to use the app and explore its functionalities interactively.We hope you find both the tool and the tutorial helpful and easy to use — whether you’re working in genomics, proteomics, or any field involving large-scale FASTA datasets.If you have feedback or questions, feel free to reach out!

📊 Explore FASTA Length Distributions with the All-in-One, Easy-to-Use SeqLengthPlot v2.0 Interactive Shiny R App

<h3>Antimicrobial resistance is a threat we can no longer ignore</h3>Antimicrobial resistance (AMR) is one of the most urgent and escalating health challenges of the 21st century, already claiming more lives annually than HIV and malaria. With forecasts projecting up to ten million deaths per year by 2050, the global need for novel, effective antimicrobial therapies is undeniable. Amid this crisis, the ocean—vast, rich, and largely unexplored—emerges as a vital source of hope. Marine ecosystems, with their extraordinary biodiversity, are home to bacteria, fungi, algae, sponges, and other organisms that produce structurally diverse and biologically potent secondary metabolites. These natural compounds, shaped by millions of years of evolution in extreme conditions, offer unprecedented chemical templates to address the limitations of current antibiotics.<figure id="figure-jlb5zoko1hm9ve18lu"><img id="jlb5zoko1hm9ve18lu" src="https://cdn.durable.co/covers/34s7inC7l1kanl7kdpLafqx8clGg6OMIDiZEukDlfRkMOWZw16Mcnc9ZW1tyNCB6.png" alt="marine life" title="marine life" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9; object-position: 100% 100%;" data-corners="default" data-aspect="16:9" data-caption="" data-positionx="100%" data-positiony="100%" data-fullwidth="false" data-mce-src="https://cdn.durable.co/covers/34s7inC7l1kanl7kdpLafqx8clGg6OMIDiZEukDlfRkMOWZw16Mcnc9ZW1tyNCB6.png" data-mce-style="aspect-ratio: 16/9; object-position: 100% 100%;"></figure><h3>a deep dive into marine solutions&nbsp;</h3>Our special issue in Frontiers in Microbiology, titled "<a data-mce-href="https://www.frontiersin.org/research-topics/64183/harnessing-marine-biodiversity-for-novel-antimicrobial-agents-against-multidrug-resistant-pathogens" href="https://www.frontiersin.org/research-topics/64183/harnessing-marine-biodiversity-for-novel-antimicrobial-agents-against-multidrug-resistant-pathogens">Harnessing Marine Biodiversity for Novel Antimicrobial Agents Against Multidrug-Resistant Pathogens</a>", brings together <a data-mce-href="https://www.frontiersin.org/research-topics/64183/harnessing-marine-biodiversity-for-novel-antimicrobial-agents-against-multidrug-resistant-pathogens/articles" href="https://www.frontiersin.org/research-topics/64183/harnessing-marine-biodiversity-for-novel-antimicrobial-agents-against-multidrug-resistant-pathogens/articles">eight original research and review articles</a>, including an <a data-mce-href="https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1607539/full" href="https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1607539/full">editorial</a> that summarizes the most significant findings. From marine-derived fungi and Arctic actinobacteria to bioengineered peptides inspired by Antarctic fish and silver nanoparticles synthesized from mollusks, the studies in this issue exemplify the chemical and therapeutic potential of marine biodiversity in the fight against multidrug-resistant pathogens.<figure id="figure-8ngmbenh5m9vfegcm"><img id="8ngmbenh5m9vfegcm" src="https://cdn.durable.co/blocks/15OtxBKeF8Ur4aEpB9U66bWygf2UqEyXximXlxfnQKijnjdgoaNkGhP5I5nvyMDl.png" alt="" title="" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 1/1; object-position: 40% 40%;" data-corners="default" data-aspect="1:1" data-caption="" data-positionx="40%" data-positiony="40%" data-fullwidth="false" data-mce-src="https://cdn.durable.co/blocks/15OtxBKeF8Ur4aEpB9U66bWygf2UqEyXximXlxfnQKijnjdgoaNkGhP5I5nvyMDl.png" data-mce-style="aspect-ratio: 1/1; object-position: 40% 40%;"></figure>This collection not only highlights the multidisciplinary innovation required to unlock marine bioactive compounds but also invites deeper reflection on the pressing threats of AMR, the growing role of microbial biofilms in treatment failure, and the urgent need to move beyond terrestrial sources in drug discovery. The featured works underscore a growing scientific consensus: the ocean is more than a biological frontier—it is a strategic resource in global health security. Yet, as this frontier unfolds, so do its complexities. The translation of marine compounds into clinically viable drugs faces hurdles such as sustainable bioprospecting, low natural yields, difficulties in isolation and synthesis, and the challenge of ecological sensitivity. These barriers demand collaborative innovation across disciplines—uniting marine biology, natural product chemistry, synthetic biology, pharmacology, bioinformatics, machine learning, AI-driven approaches and health policy.<figure id="figure-0bvezhcp4hm9ve1b62"><img id="0bvezhcp4hm9ve1b62" src="https://cdn.durable.co/getty/2698uS2ZsIG5EEC86bBuOsb0ST7b32SX58AthWhlz3oJwYuw7RGcKpUp8PxkiXqq.jpeg" alt="marine research" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9;" data-mce-src="https://cdn.durable.co/getty/2698uS2ZsIG5EEC86bBuOsb0ST7b32SX58AthWhlz3oJwYuw7RGcKpUp8PxkiXqq.jpeg" data-mce-style="aspect-ratio: 16/9;"></figure>As the AMR crisis deepens, the call for responsible, cross-sector innovation becomes ever more critical. What this special issue ultimately offers is not just a scientific snapshot, but a glimpse of a much-needed shift: one that recognizes the ocean not only as a cradle of life but as a key player in addressing one of the defining public health crises of our time.

Editorial: Harnessing Marine Biodiversity for Novel Antimicrobial Agents Against Multidrug-Resistant Pathogens

When engineering and biotechnology come together

Are you looking for an intuitive tool to streamline your sequence analysis? 🧬 <a data-mce-href="https://academic.oup.com/bioinformaticsadvances/article/5/1/vbae183/7905457" href="https://academic.oup.com/bioinformaticsadvances/article/5/1/vbae183/7905457">SeqLengthPlot v2.0.2</a> is a Python-based, all-in-one solution designed to help you visualize sequence length distributions, split sequences by customizable thresholds, and generate detailed statistics—all in one seamless workflow.<figure id="figure-t04fqdz6gim680mvrv"><img id="t04fqdz6gim680mvrv" src="https://cdn.durable.co/blocks/29lowehv0IeSEYVJqIYZOBAlN1UHkff4ZOQ3h09PQnmvgbf0fDtHkfPXWz4p1HNR.png" alt="" title="" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 1/1; object-position: 5% 5%;" data-corners="default" data-aspect="1:1" data-caption="" data-positionx="5%" data-positiony="5%" data-fullwidth="false" data-mce-src="https://cdn.durable.co/blocks/29lowehv0IeSEYVJqIYZOBAlN1UHkff4ZOQ3h09PQnmvgbf0fDtHkfPXWz4p1HNR.png" data-mce-style="aspect-ratio: 1/1; object-position: 5% 5%;"></figure>&nbsp; What Is SeqLengthPlot? SeqLengthPlot is a versatile and easy-to-use tool for analyzing sequence lengths from FASTA files. Whether you’re working with nucleotide sequences or proteins, this tool helps you:<ul><li>Visualize length distributions using linear and log-scale plots.</li><li>Retrieve sequences split by length thresholds for downstream analysis.</li><li>Generate detailed statistics on sequence length distributions. &nbsp; What’s New in SeqLengthPlot v2.0.2? The latest version introduces several enhancements to improve flexibility and user experience:</li></ul>1. Command-Line Flexibility With customizable command-line flags, users can now:<ul><li>Specify input files and output directories.</li><li>Select sequence types (nucleotide or protein).</li><li>Define plotting backends for compatibility with their operating system.</li></ul>2. Updated Default Behavior<ul><li>Nucleotide sequences are handled by default unless the --prot flag is used to indicate protein sequences.</li><li>If optional parameters are not provided, SeqLengthPlot uses intelligent defaults to ensure smooth execution. &nbsp; <h3>Key Features</h3>Mandatory Flags:</li><li>-i (input file): Path to the input FASTA file (required). Optional Flags:</li><li>-o (output directory): By default, SeqLengthPlot creates a folder in the input file’s directory based on the file name, sequence type, and threshold.</li><li>--cutoff: Customize the sequence length cutoff (default: 200).</li><li>--nt: Specify nucleotide sequences (default behavior).</li><li>--prot: Specify protein sequences, changing file extensions to .aa.</li><li>--showplot: Display plots interactively in a pop-up window (otherwise, plots are saved automatically).</li><li>--backend: Specify the plotting backend for matplotlib:TkAgg (default for Linux/Windows), and MacOSX (for macOS). &nbsp; Dependencies SeqLengthPlot requires:</li><li>Python 3.x</li><li>Matplotlib</li><li>Biopython Ensure these dependencies are installed before running the tool.</li></ul>&nbsp; Why Choose SeqLengthPlot? SeqLengthPlot v2.0.2 offers a streamlined solution for #Bioinformatics and sequence analysis tasks. Its flexibility and ease of use make it ideal for:<ul><li>Visualizing FASTA file content.</li><li>Filtering sequences by length thresholds.</li><li>Analyzing nucleotide and protein sequences with minimal setup. &nbsp; <h3>Ready to Get Started?</h3> Check out our detailed tutorial to learn how to install and run SeqLengthPlot, and start leveraging its powerful features today!</li></ul><figure id="figure-wvodxsohckm682i3zf"><iframe id="wvodxsohckm682i3zf" src="https://www.youtube.com/embed/MlFvxbHccv8" class="w-full bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9;" allowfullscreen="" data-url="https://youtu.be/MlFvxbHccv8" data-corners="default" data-fullwidth="false" data-mce-src="https://www.youtube.com/embed/MlFvxbHccv8" data-mce-style="aspect-ratio: 16/9;"></iframe></figure>For more information, visit: <a data-mce-href="https://academic.oup.com/bioinformaticsadvances/article/5/1/vbae183/7905457" href="https://academic.oup.com/bioinformaticsadvances/article/5/1/vbae183/7905457" data-mce-selected="inline-boundary">https://doi.org/10.1093/bioadv/vbae183</a>

SeqLengthPlot v2.0.2: An All-in-One, Easy-to-Use Tool for Visualizing and Retrieving Sequence Lengths from FASTA Files

a person swimming in the ocean with a mountain in the background

<h2>Cnidarian Venoms: The Bioactive Legacy of Ancient Hunters</h2>Cnidarians are a diverse group of aquatic animals. They include jellyfish, corals, and sea anemones. These creatures are known for their stinging cells, called cnidocytes. These cells help them capture prey and defend against predators, by releasing a venom secretion containing a variety of bioactive compounds.&nbsp; These compounds include toxins, peptides and non-proteincaeus substances. Scientists study these compounds for their potential applications in medicine and biotechnology.<figure id="figure-fdv9jwlvucm126os98"><img id="fdv9jwlvucm126os98" src="https://images.unsplash.com/photo-1524096613842-71a8c45f08a2?crop=entropy&amp;cs=tinysrgb&amp;fit=max&amp;fm=jpg&amp;ixid=M3wyNjI5NjF8MHwxfHNlYXJjaHwzN3x8c2VhJTIwYW5lbW9uZXxlbnwwfHx8fDE3MTMxOTMzMzB8MA&amp;ixlib=rb-4.0.3&amp;q=80&amp;w=1080" alt="orange and white fishes" title="orange and white fishes" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9; object-position: center center;" data-corners="default" data-aspect="16:9" data-caption="" data-positionx="null" data-positiony="null" data-fullwidth="false" data-mce-src="https://images.unsplash.com/photo-1524096613842-71a8c45f08a2?crop=entropy&amp;cs=tinysrgb&amp;fit=max&amp;fm=jpg&amp;ixid=M3wyNjI5NjF8MHwxfHNlYXJjaHwzN3x8c2VhJTIwYW5lbW9uZXxlbnwwfHx8fDE3MTMxOTMzMzB8MA&amp;ixlib=rb-4.0.3&amp;q=80&amp;w=1080" data-mce-style="aspect-ratio: 16/9; object-position: center center;"></figure>their potential therapeutic uses. For example, some toxins can be used as painkillers. Others may help in developing treatments for various diseases.<h3>The Unleashed Power of Cnidarian Venoms</h3>Cnidarians, the largest phylum of venomous animals, hold immense potential for medical and scientific advancements. Among them, sea anemones are particularly notable, as most characterized cnidarian toxins have been derived from these fascinating creatures. Their toxins, known for modulating nerve activity, present exciting possibilities for the development of new treatments for chronic pain, epilepsy, and autoimmune diseases. Beyond medicine, these potent compounds may also inspire the creation of environmentally friendly insecticides, offering sustainable solutions for pest control and ecological preservation.<figure id="figure-tgmkws9b0sm126otnq"><img id="tgmkws9b0sm126otnq" src="https://images.unsplash.com/photo-1520302659201-7ecf4ae863d0?crop=entropy&amp;cs=tinysrgb&amp;fit=max&amp;fm=jpg&amp;ixid=M3wyNjI5NjF8MHwxfHNlYXJjaHwyNXx8bWFyaW5lfGVufDB8fHx8MTcxMzE5MjA4N3ww&amp;ixlib=rb-4.0.3&amp;q=80&amp;w=1080" alt="purple and green coral reefs" title="purple and green coral reefs" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9; object-position: center center;" data-corners="default" data-aspect="16:9" data-caption="" data-positionx="null" data-positiony="null" data-fullwidth="false" data-mce-src="https://images.unsplash.com/photo-1520302659201-7ecf4ae863d0?crop=entropy&amp;cs=tinysrgb&amp;fit=max&amp;fm=jpg&amp;ixid=M3wyNjI5NjF8MHwxfHNlYXJjaHwyNXx8bWFyaW5lfGVufDB8fHx8MTcxMzE5MjA4N3ww&amp;ixlib=rb-4.0.3&amp;q=80&amp;w=1080" data-mce-style="aspect-ratio: 16/9; object-position: center center;"></figure><h3>Wide-Ranging Applications of Cnidarian-Derived Peptides and Toxins</h3>The bioactive compounds found in cnidarian venoms, particularly peptides derived from species like Stichodactyla helianthus, are being explored for a broad spectrum of applications. Notably, certain peptide-based toxins are currently under development as treatments for autoimmune diseases, such as ShK, a peptide that selectively targets specific ion channels involved in immune system regulation. This peptide shows great promise in treating conditions like multiple sclerosis by modulating immune responses without causing widespread immune suppression.In addition, these peptides are being investigated for their potential in creating environmentally friendly insecticides. Their unique selectivity for ion channels found in pests—but not in humans or beneficial species—makes them ideal candidates for sustainable pest control solutions. Beyond agriculture, cnidarian toxins are being studied for their use in treating neurological disorders and providing pain relief, opening new avenues for managing chronic pain and nerve-related conditions by specifically targeting nerve pathways.Moreover, cnidarians represent an underexplored source of bioactive compounds with diverse antimicrobial, antiviral, antitumor, antiparasitic, and antibiofilm properties. This untapped chemical diversity holds tremendous potential for the development of new therapeutics and biotechnological applications, further highlighting the vast promise of cnidarian venoms in medicine and beyond.<figure id="figure-hf6hp7s1zcm126oulm"><img id="hf6hp7s1zcm126oulm" src="https://images.unsplash.com/photo-1582560475093-ba66accbc424?crop=entropy&amp;cs=tinysrgb&amp;fit=max&amp;fm=jpg&amp;ixid=M3wyNjI5NjF8MHwxfHNlYXJjaHwxMHx8bWVkaWNhbCUyMHJlc2VhcmNofGVufDB8fHx8MTcyNjMxMDM1NHww&amp;ixlib=rb-4.0.3&amp;q=80&amp;w=1080" alt="medical research" class="object-cover bg-gray-100 rounded-sm md:rounded-md lg:rounded-lg" style="aspect-ratio: 16/9;" data-mce-src="https://images.unsplash.com/photo-1582560475093-ba66accbc424?crop=entropy&amp;cs=tinysrgb&amp;fit=max&amp;fm=jpg&amp;ixid=M3wyNjI5NjF8MHwxfHNlYXJjaHwxMHx8bWVkaWNhbCUyMHJlc2VhcmNofGVufDB8fHx8MTcyNjMxMDM1NHww&amp;ixlib=rb-4.0.3&amp;q=80&amp;w=1080" data-mce-style="aspect-ratio: 16/9;"></figure><h2>Current Status and Future Directions in the Biodiscovery of Cnidarian Toxins and Bioactive Peptides </h2>Herein, we are launching a Special Issue titled "<a data-mce-href="https://www.mdpi.com/journal/toxins/special_issues/TAL5WM104S" href="https://www.mdpi.com/journal/toxins/special_issues/TAL5WM104S">Current Status and Future Directions in the Biodiscovery of Canonical Toxins and Bioactive Peptides from Cnidarians</a>," in collaboration with guest editors Guillermin Aguero-Chapin, Professor Olga Castañeda Pasarón, and Maria Vittoria Modica. Published in the journal Toxins, this issue seeks to provide an updated exploration of the diverse cnidarian toxins, advanced methodologies for their study, and their applications in biotechnology.We invite researchers specializing in cnidarian bioactive compounds, venom analysis, and omics technologies to submit their contributions, helping to expand our understanding of these marine organisms and guide future directions in toxin research.

Exploring Toxins and Bioactive Peptides from Cnidarians

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Exploring Toxins and Bioactive Peptides from Cnidarians