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PubMed1990

Bifurcation analysis of nonlinear retinal horizontal cell models. II. Network properties.

1. We have previously presented a model of horizontal-cell soma isolated from fish retina. The model consists of a synaptic conductance representing input from photoreceptors in parallel with voltage-dependent membrane currents. Membrane-current models are based on I-V curves measured in isolated fish horizontal cells. Bifurcation theory was used to analyze model properties. The major findings of this study were 1) the inward Ca2+ current must be inactivated to account for horizontal-cell resting potentials and hyperpolarizing responses to light stimuli in a background of dark, and 2) the synaptic conductance controls the bifurcation structure of the model, with bistable behavior occurring at small and monostable behavior occurring at larger values of the synaptic conductance. The synaptic conductance at the point of transition from bistable to monostable behavior corresponds to the activation of as few as 100 synaptic channels. Thus tonic synaptic input from photoreceptors and inactivation of the inward Ca2+ current act to "linearize" responses of isolated horizontal-cell models. 2. The model described in this paper extends these analyses to large networks of horizontal cells in which each cell is coupled resistively to its nearest neighbors and is modeled with the use of the full complement of nonlinear membrane currents. Network responses to arbitrary patterns of conductance change (simulating inputs from photoreceptors), current-, or voltage-clamp stimuli are computed using the Newton iteration. The Newton descent direction is computed using either conjugate gradient (CG) or preconditioned CG algorithms. 3. An analysis of network stability properties is performed. Network I-V curves are computed by voltage-clamping the center node and computing the current required to maintain the clamp voltage. Computations are performed on networks of model cells in which the Ca2+ current is fully activated and the synaptic conductance is zero, thus making each cell as nonlinear as possible. Coupling conductance values slightly greater than 100 pS provide a current shunt sufficient to prevent the generation of Ca2+ action potentials in the network. This coupling conductance corresponds to the conductance of as few as two gap-junction channels and is more than two orders of magnitude less than the coupling known to exist between pairs of cultured horizontal cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1989

A parallel implementation of the ALOPEX process.

Optimization techniques have found many applications in science, engineering, and industry. In all applications, the best value of a "cost function" is sought in a well-defined domain; this cost function in general depends on many parameters. An iterative optimization technique has been developed (ALOPEX) that uses feedback in order to optimize the response of a system. The cost function for this process is problem dependent and therefore quite flexible. The method has been applied successfully to different optimization problems such as pattern recognition, receptive field studies in the visual system of animals, curve fitting, etc. We present two special purpose hardware implementations for ALOPEX. The first method takes time O(logN + logm) and uses O(mN2) processing elements. The second method takes O(logN + m) time and uses O(N2) processing elements. Our basic architecture is a binary tree with N2 leaves (equal to the length of the vectors) and therefore had depth O(logN). Different implications of the two approaches will be discussed including similarities with the biological visual process.

Algorithms↗
PubMed1992

Droop: a rapidly computable descriptor of local minimum tissue temperature during conductive interstitial hyperthermia.

Although the goal of local hyperthermia therapy for cancer is to elevate the temperature of a tumour to cytotoxic levels, without the presence of 'cold spots', varying blood flow has made the achievement of consistent, therapeutic temperature distributions extraordinarily difficult. The paper presents a novel approach to estimating local minimum tumour temperatures during conductive interstitial hyperthermia which facilitates identification and elimination of cold spots. Conductive interstitial hyperthermia is modelled mathematically for a parallel array of implanted, electrically heated catheters which warms the treated tissue by thermal conduction and blood perfusion. Computer simulations employing the bioheat transfer equation reveal a predictive relationship between implanted catheter temperature, catheter power, implantation geometry and local minimum tumour temperature. Formulation of this relationship in terms of a parameter named 'droop' allows estimation of local minimum intratumoural temperatures from individual catheter temperature and power. Computer simulations are also performed to determine the sensitivity of the droop-based estimator to variations in properties of the tissue and catheters. Generally, variations in geometry or thermal properties of about 10 per cent cause estimation errors of less than 1 degree C in magnitude. These results suggest that online estimates of thermal 'droop' may provide a practical route to more consistent control of intratumoural minimum temperature during conductive interstitial heat therapy.

Algorithms↗
PubMed1990

Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins.

The preferred structural pattern of antiparallel beta-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of beta-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel beta-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted beta-barrel is favored energetically, in agreement with anti-parallel beta-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of beta-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel beta-barrels of globular proteins. The computations indicate that a structure with Val...Gly pairs can be accommodated in a beta-barrel with no distortion.

Algorithms↗
PubMed1989

Three-dimensional image reconstruction from complete projections.

Three-dimensional medical image reconstruction for both transmission and emission tomography has traditionally decomposed the problem into a set of two-dimensional reconstructions on parallel transverse sections. There is, however, increasing interest in reconstructing projection data directly in three dimensions. For emission tomography in particular, such a reconstruction procedure would clearly make more efficient use of the available photon flux. In the past few years, a number of authors have studied the problems associated with full three-dimensional reconstruction, especially in the case of positron tomography where three-dimensional reconstruction is likely to offer the greatest benefits. While most approaches follow that of filtered backprojection, the relationship between the various filters that have been proposed is far from evident. This paper clarifies this relationship by analysing and generalising the different classes of published filters and establishes the properties and characteristics of a general solution to the three-dimensional reconstruction problem. Some guidelines are suggested for the choice of an appropriate filter in a given situation.

Algorithms↗
PubMed1988

Effect of Ca2+ on cross-bridge turnover kinetics in skinned single rabbit psoas fibers: implications for regulation of muscle contraction.

The effect of Ca2+ upon the rate constant of force redevelopment following a period of isotonic shortening with immediate restretch to the starting sarcomere length was studied in rabbit psoas fibers at 5 degrees C. Control experiments support the assumption that the rate constant of force redevelopment represents isometric cross-bridge turnover kinetics (fapp + gapp), where fapp and gapp are the rate constants characterizing the transitions from the non-force-generating states to the force-generating states and back to the non-force-generating states, respectively. Parallel measurements of the rate constant of force redevelopment and of force, stiffness, and fiber ATPase during isometric contraction allow the effect of Ca2+ upon fapp and gapp to be determined. Analysis reveals that Ca2+ has a marked effect upon fapp, while gapp remains approximately unchanged. Furthermore, in the range above 25-30% of maximum Ca2+ activation, regulation of force, stiffness, and ATPase is mediated through changes in fapp. Below this range, however, it cannot be ruled out that, in addition, cross-bridges are also switched in and out of the turnover process ("recruitment"). As a consequence of regulation through turnover kinetics, both Ca2+ sensitivity and the slope of force-pCa (-log[Ca2+]) relations are shown to be affected by the ratio fapp/gapp, which may represent an important mechanism of modulation of contractile function in addition to modulation through changes within the regulatory protein system.

Adenosine Triphosphatases↗
PubMed2025

Columba: fast approximate pattern matching with optimized search schemes.

MOTIVATION: Aligning sequencing reads to reference genomes is a fundamental task in bioinformatics. Aligners can be classified as lossy or lossless: lossy aligners prioritize speed by reporting only one or a few high-scoring alignments, whereas lossless aligners output all optimal alignments, ensuring completeness and sensitivity. RESULTS: This paper introduces Columba, a high-performance lossless aligner tailored for Illumina sequencing data. Columba processes single or paired-end reads in FASTQ format and outputs alignments in SAM format. By utilizing advanced search schemes and bit-parallel alignment techniques, Columba achieves exceptional speed. Columba is available in two variants. The first, based on the bidirectional FM-index, prioritizes speed. The second, Columba RLC, uses run-length compression using a bidirectional move structure, significantly reducing memory usage for large, repetitive datasets like pan-genomes. Benchmarks on the human genome, as well as bacterial and human pan-genome datasets, demonstrate that Columba is much faster than existing lossless aligners and even competitive with lossy tools. We integrated Columba into the OptiType HLA genotyping pipeline, where it substantially reduced computational time while maintaining accuracy. These results position Columba as a versatile, state-of-the-art tool for high-sensitivity genomic analyses. AVAILABILITY AND IMPLEMENTATION: The source code of Columba is available at https://github.com/biointec/columba under AGPL license. Scripts to reproduce the benchmarks and analyses are available at https://doi.org/10.5281/zenodo.15849246.

Software↗
PubMed1989

3-D superposition for radiotherapy treatment planning using fast Fourier transforms.

Currently used radiotherapy treatment planning algorithms based on effective path length or scatter function methods do not model electron ranging from photon interaction sites. The superposition (or convolution) technique does model this effect, which is especially important at higher (linear accelerator) energies since the electron range is significant. Another advantage of this method is that it is conceptually simple and models the physical processes directly, rather than using empirically derived methods. A major disadvantage of superposition lies in the large amount of computer time required to generate a plan, especially in three dimensions. To help solve this problem, superposition using an invariant dose spread array (kernel) can be achieved by performing a convolution in Fourier space using fast Fourier transforms (FFTs). A method for 3 dimensional calculation of dose using FFTs is presented. Dose spread arrays are calculated using the EGS Monte Carlo code, and convolved with the TERMA (total energy released per unit mass). In both cases a 10 MV nominal beam energy is modelled by a 10 component spectrum, which is compared to the result obtained using monochromatic energy only (3.0 MeV at the surface). The FFT technique is shown to be significantly faster than standard convolution for medium to large TERMA and dose spread array sizes. The method is shown to be highly accurate for small fields in homogeneous media. For larger fields the central axis depth dose is accurate but the profile shape in the penumbral region becomes slightly distorted. This is because photons incident near the beam edges are not parallel to the cartesian coordinate system used as the convolution framework. However, this effect is sufficiently small to indicate that the convolution method is suitable for use in routine treatment planning.

Fourier Analysis↗
PubMed2026

PanForest: predicting genes in genomes using random forests.

MOTIVATION: The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding these gene co-occurrence and avoidance patterns reveals fundamental principles of genome organization, with applications ranging from evolutionary reconstruction to rational design of synthetic genomes. RESULTS: PanForest, presented here, uses random forest classifiers to predict the presence and absence of genes in genomes from the set of other genes present. Performance statistics output by PanForest reveal how predictable each gene's presence or absence is, based on the presence or absence of other genes in the genome. Further, PanForest produces statistics indicating the importance of each gene in predicting the presence or absence of each other gene. The PanForest software can run serially or in parallel, thereby facilitating the analysis of pangenomes at Network of Life scale.A pangenome of 12 741 accessory genes in 1000 Escherichia coli genomes was analysed in around 5 h using eight processors. To demonstrate PanForest's utility, we present a case study and show that certain genes associated with resistance to antimicrobial drugs reliably predict the presence or absence of other genes associated with resistance to the same drug. Further, we highlight several associations between those genes and others not known to be associated with antimicrobial resistance (AMR), or associated with resistance to other drugs. We envisage PanForest's use in studies from multiple disciplines concerning the dynamics of gene distributions in pangenomes ranging from biomedical science and synthetic biology to molecular ecology. AVAILABILITY AND IMPLEMENTATION: The software if freely available with a full manual and can be found with at www.github.com/alanbeavan/PanForest DOI: https://doi.org/10.5281/zenodo.17865482.

Software↗
PubMed1992

Adaptive rate pacing controlled by the right ventricular preejection interval: clinical experience with a physiological pacing system.

In the Precept pacing system, the right ventricular intracardiac impedance waveform is used to evaluate either of two indicators of metabolic demand relative right ventricular stroke volume and preejection interval (PEI). PEI is known to reliably parallel contractility changes, which is reflective of physical and emotional stress. The stability and dynamic behavior of PEI were tested in ten patients with a Precept pacing system under various forms of exercise and during postural changes. Although significant patient-to-patient variability of the sensor values was observed, reflecting individual physiological differences, the chronic stability of PEI was excellent in the total device experience of 147 months. In all patients, PEI shortened significantly during bicycle ergometry from a mean value of 137.7 +/- 17.8 (range 96-162) to a mean value of 103.0 +/- 21.6 (range 92-109) (P less than 0.05). Low level bicycle exercise of short duration resulted in a prompt decrease in PEI and increase in pacing rate in all patients. There were no uniform postural responses overall, although some posture related rate changes were observed in two patients. We conclude that the first generation of a PEI based pacing system holds promise for adaptive rate pacing.

Aged↗
PubMed1992

Artificial neural network classification of Drosophila courtship song mutants.

Courtship songs produced by Drosophila males--wild-type, plus the cacophony and dissonance behavioral mutants--were examined with the aid of newly developed strategies for adaptive acoustic analysis and classification. This system used several techniques involving artificial neural networks (a.k.a. parallel distributed processing), including learned vector quantization of signals and non-linear adaption (back-propagation) of data analysis. "Pulse" song from several individual wild-type and mutant males were first vector-quantized according to their frequency spectra. The accumulated quantized data of this kind, for a given song, were then used to "teach" or adapt a multiple-layered feedforward artificial neural network, which classified that song according to its original genotype. Results are presented on the performance of the final adapted system when faced with novel test data and on acoustic features the system decides upon for predicting the song-mutant genotype in question. The potential applications and extensions of this new system are discussed, including how it could be used to screen for courtship mutants, search novel behavior patterns or cause-and-effect relationships associated with reproduction, compress these kinds of data for digital storage, and analyze Drosophila behavior beyond the case of courtship song.

Algorithms↗
PubMedDate not supplied

Superposition on a multicomputer system.

Superposition (convolution using a noninvariant kernel) has been shown to be a highly promising technique for use in calculating dose distributions in radiotherapy treatment planning. However, one major difficulty that currently prevents use in routine planning is the computational effort required to perform the calculation in three dimensions. To help solve this problem the superposition technique has been implemented on a parallel processor multicomputer in order to examine the performance characteristics of such a system. Up to eight elements have been connected in a pipeline (linear array), and tree networks of three and seven processors have also been constructed (using INMOS T800 transputers). The significant results obtained with these networks are: (1) Both topologies provide near-linear speedup with increasing processor number (8 processors provide 7.81 times the computing power of a single processor when using an optimal communication packet size); (2) increasing communication packet size from 1 voxel to an optimum of approximately 40 voxels significantly reduces communication overhead per processor. Overhead per processor for a 7-element linear array is 6.9% when using 1-voxel packets, but only 1.8% when using 40-voxel packets; (3) the topology of the network has some effect on communication overhead: Arranging 7 processors in a 1-2-4 binary tree reduces overhead to 80.1% of that encountered using a 7-element linear array (with packet size of 1 voxel).

Algorithms↗
PubMed2025

Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture.

MOTIVATION: The wide range of cellular complexity created by multicellular organisms is due in large part to the intricate and synergistic interplay of regulatory complexes throughout the eukaryotic genome. These regulatory elements "enhance" specific gene programs and have been shown to operate in diverse networks that are distinct across cell states of the same organism. Attempts to characterize and predict enhancers have typically focused on leveraging information-dense DNA sequence in parallel with epigenomic assays. We examined the viability of enhancer prediction using only a minimal set of epigenomic datasets without direct DNA information. RESULTS: We demonstrate that chromatin datasets are sufficient to identify enhancers genome-wide with high accuracy. By training networks leveraging data from multiple cell types simultaneously, we generated a cell-type invariant enhancer prediction platform that utilized only the patterns of protein binding for inference. We also showed the utility of swarm-based adversarial attacks [adversarial particle swarm optimization (APSO)] to deconvolute trained genomic neural networks for the first time. Critically, unlike saliency mapping or other game-theory based approaches, APSO is completely network-architecture independent and can be applied to any prediction engine to derive the features that drive inference. AVAILABILITY AND IMPLEMENTATION: All software and code for data downloading, processing, enhancer inference, eXplainable AI (XAI), and complete figure generation are publicly available on GitHub at https://github.com/EpiGenomicsCode/ChromEnhancer and Zenodo at https://doi.org/10.5281/zenodo.15652797.

Enhancer Elements, Genetic↗
PubMed1988

Gallamine allosterically antagonizes muscarinic receptor-mediated inhibition of adenylate cyclase activity in the rat myocardium.

The ability of gallamine to modify muscarinic receptor binding properties and to antagonize muscarinic receptor-mediated inhibition of adenylate cyclase activity was investigated in the rat myocardium. Gallamine caused parallel shifts to the right in the dose-response curves for inhibition of adenylate cyclase activity by the highly efficacious muscarinic agonist oxotremorine-M and the partial agonist Bm 5 [N-methyl-N-(1-methyl-4-pyrrolidino)-2-butynyl acetamide]. The nature of this effect was inconsistent with competitive inhibition, but could be explained by allosteric antagonism. Similar dissociation constants of 0.52 and 0.83 microM were estimated for gallamine on the basis of its ability to antagonize responses to oxotremorine-M and Bm 5, respectively. The maximum shift in the dose-response curve of Bm 5 caused by gallamine was 90-fold, whereas that of oxotremorine-M was only 49-fold. When measured by inhibition of the binding of the specific muscarinic antagonist [3H]N-methylscopolamine, the dissociation constant of gallamine was estimated to be 1.1 microM. The present results illustrate good agreement between the ability of gallamine to modify muscarinic receptor binding properties and to antagonize muscarinic receptor-mediated inhibition of adenylate cyclase activity in the rat heart.

Adenylyl Cyclase Inhibitors↗
PubMed2026

Sassy: fuzzy searching DNA sequences using SIMD.

MOTIVATION: Approximate string matching (ASM) is the problem of finding all occurrences of a pattern in a text while allowing up to k errors. Many modern methods use seed-chain-extend, which is fast in practice, but does not guarantee finding all matches with ≤k errors. However, applications such as CRISPR off-target detection require exhaustive results. RESULTS: We introduce Sassy, a library and tool for ASM of short patterns in long texts. Sassy splits the text into four parts that are searched in parallel, and uses bitvectors in the text direction rather than the pattern direction. This has complexity O(k⌈n/W⌉) when searching a random text of length n, where W=256 is the SIMD width, and provides significant speedups for small k. Separately, we allow matches of the pattern to extend beyond the text for an overhang cost of, e.g. α=0.5 per character, to find matches near contig or read ends.Sassy is 4× to 15× faster than Edlib for patterns ≤1000 bp, and can search text with a throughput near 2 Gbp/s. Likewise, Sassy is over 100× faster than parasail. We apply Sassy to CRISPR off-target detection by searching 61 guide sequences in a human genome. Sassy is 100× faster than SWOffinder and only slightly slower (for k≤3) than CHOPOFF, for which building its index takes 20 min. Sassy also scales well to larger k, unlike CHOPOFF whose index took over 10 h to build for k=5. AVAILABILITY AND IMPLEMENTATION: Sassy is available as library and binary at https://github.com/RagnarGrootKoerkamp/sassy, and archived at swh:1:dir:e884758dce5777a441bc2799dc8824e563c5f97b.

Sequence Analysis, DNA↗
PubMed1991

Structure of the detergent phase and protein-detergent interactions in crystals of the wild-type (strain Y) Rhodobacter sphaeroides photochemical reaction center.

Rhodobacter sphaeroides (strain Y) reaction center (RC) crystals were grown in the presence of n-octyl beta-glucoside (beta-OG). In order to determine the structure of the detergent phase in these crystals, low-resolution neutron diffraction experiments were performed at different contrasts obtained by varying the H2O/D2O ratio in the solvent. From the contrast variation data and from the RC atomic coordinates determined by X-ray diffraction [Arnoux, B., Ducruix, A., Reiss-Husson, F., Lutz, M., Norris, J., Schiffer, M., & Chang, C. H. (1989) FEBS Lett. 258, 47-50], a model was obtained for the structure of the detergent phase in the crystal. The detergent forms a ring-shaped micelle surrounding the most hydrophobic part of the transmembrane alpha helices of the RC. Each detergent ring is connected to two next-neighbor rings by intermicellar bridges. The detergent phase is organized thus in infinite zigzag chains parallel to the b axis of the P2(1)2(1)2(1) unit cell. The main interactions between beta-OG molecules and the RC molecules are hydrophobic and are localized at the level of the transmembrane alpha helices. This interaction replaces the phospholipid-protein interaction existing in vivo in the membrane and, to some extent, also the light harvesting complex-protein interaction. Secondary hydrophilic interactions are found between a few of the charged residues of the H subunit and the hydrophilic surface of the detergent ring from a neighboring RC molecule. A comparison with a previous study on Rhodopseudomonas viridis crystals [which grow in the presence of lauryldimethylamine N-oxide (LDAO) and belong to a different space group] [Roth, M., Lewit-Bentley, A., Michel, H., Deisenhofer, J., Huber, R., & Oesterhelt, D. (1989) Nature 340, 659-661] shows a quasi identity of shape and position of the beta-OG and LDAO rings around the transmembrane alpha helices. The secondary interactions, involving in both cases the external surface of the H subunit, differ because of the different molecular packing in the two space groups. The role and structural requirements of the detergent in the crystallization process are discussed.

Algorithms↗
PubMed1987

Multiple actions of cadmium on transmitter release at the mouse neuromuscular junction.

The action of cadmium ions on transmitter release was studied at the neuromuscular junction in mouse diaphragm. In the presence of raised K+, Cd2+ caused a parallel shift to the right of the graph of transmitter release rate (frequency of miniature end-plate potentials, fmepp) versus log [Ca2+], with no change in maximum or slope, indicating a competitive mode of action of Cd2+. The apparent dissociation constant for Cd2+ was 3 microM. In calcium-free solutions containing 15 mM K+, Cd2+ caused a rise in the fmepp, which subsequently slowly declined despite the continued presence of Cd2+. The rise in fmepp caused by Cd2+ could be interrupted, but not reversed, by washing out the Cd2+ with EDTA. Exposure of the preparation to 100 microM Cd2+ for 15 min or more resulted in a raised fmepp that persisted despite the removal of Cd2+ and exposure to 200 microM EDTA. Following such treatment, the graph of fmepp versus log [Ca2+] continued to be shifted to the right. The interaction of Ca2+ with the residual effect of Cd2+ indicates that Cd2+, in addition to its action to block Ca2+ entry into the terminal, may act as a competitor and perhaps as a partial agonist at intracellular sites that normally bind Ca2+ and govern transmitter release. If this is the case, then it must be supposed that, in raised K+, quantal release of transmitter represents intermittent intense activation of release sites with local high levels of Ca2+ rather than continuous low level activation.

Algorithms↗
PubMed2025

polars-bio-fast, scalable, and out-of-core operations on large genomic interval datasets.

MOTIVATION: Genomic studies very often rely on computationally intensive analyses of relationships between features, which are typically represented as intervals along a 1D coordinate system (such as positions on a chromosome). In this context, the Python programming language is extensively used for manipulating and analyzing data stored in a tabular form of rows and columns, called a DataFrame. Pandas is the most widely used Python DataFrame package and has been criticized for inefficiencies and scalability issues, which its modern alternative-Polars-aims to address with a native backend written in the Rust programming language. RESULTS: polars-bio is a Python library that enables fast, parallel and out-of-core operations on large genomic interval datasets. Its main components are implemented in Rust, using the Apache DataFusion query engine and Apache Arrow for efficient data representation. It is compatible with Polars and Pandas DataFrame formats. In a real-world comparison (107 versus 1.2×106 intervals), our library runs overlap queries 6.5×, nearest queries 15.5×, count_overlaps queries 38×, and coverage queries 15× faster than Bioframe. On equally sized synthetic sets (107 versus 107), the corresponding speedups are 1.6×, 5.5×, 6×, and 6×. In streaming mode, on real and synthetic interval pairs, our implementation uses 90× and 15× less memory for overlap, 4.5× and 6.5× less for nearest, 60× and 12× less for count_overlaps, and 34× and 7× less for coverage than Bioframe. Multi-threaded benchmarks show good scalability characteristics. To the best of our knowledge, polars-bio is the most efficient single-node library for genomic interval DataFrames in Python. AVAILABILITY AND IMPLEMENTATION: polars-bio is an open-source Python package distributed under the Apache License available for major platforms, including Linux, macOS, and Windows in the PyPI registry. The online documentation is https://biodatageeks.org/polars-bio/ and the source code is available on GitHub: https://github.com/biodatageeks/polars-bio and Zenodo: https://doi.org/10.5281/zenodo.16374290. are available at Bioinformatics online.

Software↗