Logs are crucial for analyzing large-scale software systems, offering insights into system health, performance, security threats, potential bugs, etc. However, their chaotic na-ture-characterized by sheer volume, lack of standards, and variability-makes manual analysis complex. The use of clustering algorithms can assist by grouping logs into a smaller set of templates, but lose the temporal and relational context in doing so. On the contrary, Large Language Models (LLMs) can provide meaningful explanations but struggle with processing large collections efficiently. Moreover, representation techniques for both approaches are typically limited to either plain text or traditional charting, especially when dealing with large-scale systems. In this paper, we combine clustering and LLM summarization with event detection and Multidimensional Scaling through the use of Time Curves to produce a holistic pipeline that enables efficient and automatic summarization of vast collections of software system logs. The core of our approach is the proposal of a semimetric distance that effectively measures similarity between events, thus enabling a meaningful representation. We show that our method, based on logs collected from different applications, can explain the behavior of a system over time without prior knowledge. We also show how the approach can be used to detect general trends as well as outliers in parallel and distributed systems by overlapping multiple projections. As a result, we expect a significant reduction in the time required to analyze system-wide issues, identify performance bottlenecks and security risks, debug applications, etc.

Abstract The use of Graphics Processing Units to accelerate computational applications is increasingly being adopted due to its affordability, flexibility and performance. However, achieving top performance comes at the price of restricted data-parallelism models. In the case of sequence alignment, most GPU-based approaches focus on accelerating the Smith-Waterman dynamic programming algorithm due to its regularity. Nevertheless, because of its quadratic complexity, it becomes impractical when comparing long sequences, and therefore heuristic methods are required to reduce the search space. We present GPUGECKO, a CUDA implementation for the sequential, seed-and-extend sequence-comparison algorithm, GECKO. Our proposal includes optimized kernels based on collective operations capable of producing arbitrarily long alignments while dealing with heterogeneous and unpredictable load. Contrary to other state-of-the-art methods, GPUGECKO employs a batching mechanism that prevents memory exhaustion by not requiring to fit all alignments at once into the device memory, therefore enabling to run massive comparisons exhaustively with improved sensitivity while also providing up to 6x average speedup w.r.t. the CUDA acceleration of BLASTN.

MOTIVATION: Molecular docking is aimed at predicting the conformation of small-molecule (ligands) within an identified binding site (BS) in a target protein (receptor). Protein-ligand docking plays an important role in modern drug discovery and biochemistry for protein engineering. However, efficient docking analysis of proteins requires prior knowledge of the BS, which is not always known. The process which covers BS identification and protein-ligand docking usually requires the combination of different programs, which require several input parameters. This is furtherly aggravated when factoring in computational demands, such as CPU-time. Therefore, these types of simulation experiments can become a complex process for researchers without a background in computer sciences. RESULTS: To overcome these problems, we have designed an automatic computational workflow (WF) to process protein-ligand complexes, which runs from the identification of the possible BSs positions to the prediction of the experimental binding modes and affinities of the ligand. This open-access WF runs under the Galaxy platform that integrates public domain software. The results of the proposed method are in close agreement with state-of-the-art docking software. AVAILABILITY AND IMPLEMENTATION: Software is available at: https://pistacho.ac.uma.es/galaxy-bitlab. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Motivation: Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Results: Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. Availability and implementation: mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. Contact: [email protected]. Supplementary information: Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca.