Herald:The Biostar Herald for Monday, February 03, 2025
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The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.

This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,


Akshay Agrawal on Twitter: On Jupyter Notebooks (x.com)

Jupyter notebooks suffer from a reproducibility crisis — just 4% of notebooks on GitHub reproduce.

That's why @Stanford researchers decided the world needed a new open-source Python notebook.

The result was @marimo_io Learn more in our blog

submitted by: Istvan Albert


Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2 | BMC Genomics | Full Text (bmcgenomics.biomedcentral.com)

Finding orthologs remains an important bottleneck in comparative genomics analyses. Here we compared RBH results obtained using software that runs faster than blastp. Namely, lastal, diamond, and MMseqs2 The fast algorithms for pairwise protein comparison produced results very similar to blast in a fraction of the time, with diamond offering the best compromise in speed, sensitivity and quality, as long as a sensitivity option, other than the default, was chosen.

GitHub: https://github.com/Computational-conSequences/SequenceTools

submitted by: Istvan Albert


PSAURON: a tool for assessing protein annotation across a broad range of species (academic.oup.com)

In this manuscript, we introduce PSAURON (Protein Sequence Assessment Using a Reference ORF Network), a novel software tool developed to help assess the quality of protein-coding gene annotations. Utilizing a machine learning model trained on a diverse dataset from over 1000 plant and animal genomes, PSAURON assigns a score to coding DNA or protein sequence that reflects the likelihood that the sequence is a genuine protein-coding region.

Github: https://github.com/salzberg-lab/PSAURON

submitted by: Istvan Albert


How should the advancement of large language models affect the practice of science? (www.pnas.org)

For this opinion piece, we have invited four diverse groups of scientists to reflect on this query, sharing their perspectives and engaging in debate.

  1. Schulz et al. make the argument that working with LLMs is not fundamentally different from working with human collaborators,
  2. Bender et al. argue that LLMs are often misused and overhyped, and that their limitations warrant a focus on more specialized, easily interpretable tools.
  3. Marelli et al. emphasize the importance of transparent attribution and responsible use of LLMs.

  4. Botvinick and Gershman advocate that humans should retain responsibility for determining the scientific roadmap.

submitted by: Istvan Albert


BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow | bioRxiv (www.biorxiv.org)

Achieving effective workflow automation requires robust task coordination, dynamic knowledge retrieval, and mechanisms to ensure errors are identified and resolved before they impact downstream processes. We present BioMaster, a multi-agent framework designed to automate and streamline complex bioinformatics workflows. BioMaster incorporates specialized agents with role-based responsibilities, enabling precise task decomposition, execution, and validation.

Editor's note: I am hugely skeptical - but then it is our jobs on the line :-) so of course I am skeptical ...

submitted by: Istvan Albert


Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer | Nature Communications (www.nature.com)

Whole-genome sequencing of 51 tumors revealed intratumor heterogeneity of HPV integration, with 44% of breakpoints subclonal, and a biased distribution of integration breakpoints across the HPV genome. Four HPV physical states were identified, with at least 49% of tumors progressing without integration. HPV integration was associated with APOBEC-induced broad genomic instability and focal genomic instability, including structural variants at integration sites.

submitted by: Istvan Albert


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