scholarly journals Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

2017 ◽  
Vol 18 (S10) ◽  
Author(s):  
Marwan Abdellah ◽  
Juan Hernando ◽  
Nicolas Antille ◽  
Stefan Eilemann ◽  
Henry Markram ◽  
...  
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Optical Studies ◽  
Volumetric Models

scholarly journals Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

2017 ◽  
Author(s):  
Marwan Abdellah ◽  
Juan Hernando ◽  
Nicolas Antille ◽  
Stefan Eilemann ◽  
Henry Markram ◽  
...  
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Circuit Model ◽  
Optical Studies ◽  
Domain Experts ◽  
Multi Stage ◽  
Volumetric Models ◽  
Imaging Experiment ◽  
Cortical Circuit ◽  
Tissue Models

AbstractBackground We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons. The limitations of the existing approaches for creating those models are explained, and then, a multi-stage pipeline is discussed to overcome those limitations. Starting from the neuronal morphologies, we create smooth piecewise watertight polygonal models that can be efficiently utilized to synthesize continuous and plausible volumetric models of the neurons with solid voxelization. The somata of the neurons are reconstructed on a physically-plausible basis relying on the physics engine in Blender.Results Our pipeline is applied to create 55 exemplar neurons representing the various morphological types that are reconstructed from the somatsensory cortex of a juvenile rat. The pipeline is then used to reconstruct a volumetric slice of a cortical circuit model that contains ∼210,000 neurons. The applicability of our pipeline to create highly realistic volumetric models of neocortical circuits is demonstrated with an in silico imaging experiment that simulates tissue visualization with brightfield microscopy. The results were evaluated with a group of domain experts to address their demands and also to extend the workflow based on their feedback.Conclusion A systematic workflow is presented to create large scale synthetic tissue models of the neocortical circuitry. This workflow is fundamental to enlarge the scale of in silico neuroscientific optical experiments from several tens of cubic micrometers to a few cubic millimeters.

scholarly journals Large-scale synapse-level neuronal wiring diagrams in silico and in vitro

2008 ◽  
Vol 9 (S1) ◽  
Author(s):  
Upinder S Bhalla ◽  
Radhika Madhavan ◽  
Ashesh Dhawale ◽  
Mehrab Modi ◽  
Raamesh Deshpande ◽  
...  
Keyword(s):  
In Silico ◽  
Large Scale

Large-scale in silico screening of compounds contained in printing inks for food packaging materials

2018 ◽  
Vol 295 ◽  
pp. S96
Author(s):  
M. Smieško ◽  
C. Don ◽  
R. Meuwly ◽  
S. Kucsera ◽  
B.J. Brüschweiler
Keyword(s):  
In Silico ◽  
Food Packaging ◽  
Large Scale ◽  
Packaging Materials ◽  
In Silico Screening ◽  
Food Packaging Materials ◽  
Printing Inks

scholarly journals Accurate long-read de novo assembly evaluation with Inspector

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Chen ◽  
Yixin Zhang ◽  
Amy Y. Wang ◽  
Min Gao ◽  
Zechen Chong
Keyword(s):  
Genome Assembly ◽  
De Novo Assembly ◽  
In Silico ◽  
Large Scale ◽  
De Novo ◽  
Small Scale ◽  
De Novo Genome Assembly ◽  
Consensus Sequences ◽  
Assembly Evaluation ◽  
Long Read

AbstractLong-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors.

scholarly journals X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis

2020 ◽  
Author(s):  
Dongyu Xue ◽  
Han Zhang ◽  
Dongling Xiao ◽  
Yukang Gong ◽  
Guohui Chuai ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
In Silico ◽  
Large Scale ◽  
De Novo ◽  
Representation Learning ◽  
Training Data ◽  
Fine Tuning ◽  
Model Interpretation ◽  
Unlabelled Data ◽  
Super Computing

AbstractIn silico modelling and analysis of small molecules substantially accelerates the process of drug development. Representing and understanding molecules is the fundamental step for various in silico molecular analysis tasks. Traditionally, these molecular analysis tasks have been investigated individually and separately. In this study, we presented X-MOL, which applies large-scale pre-training technology on 1.1 billion molecules for molecular understanding and representation, and then, carefully designed fine-tuning was performed to accommodate diverse downstream molecular analysis tasks, including molecular property prediction, chemical reaction analysis, drug-drug interaction prediction, de novo generation of molecules and molecule optimization. As a result, X-MOL was proven to achieve state-of-the-art results on all these molecular analysis tasks with good model interpretation ability. Collectively, taking advantage of super large-scale pre-training data and super-computing power, our study practically demonstrated the utility of the idea of “mass makes miracles” in molecular representation learning and downstream in silico molecular analysis, indicating the great potential of using large-scale unlabelled data with carefully designed pre-training and fine-tuning strategies to unify existing molecular analysis tasks and substantially enhance the performance of each task.

scholarly journals A billion synthetic 3D-antibody-antigen complexes enable unconstrained machine-learning formalized investigation of antibody specificity prediction

2021 ◽  
Author(s):  
Philippe Auguste Robert ◽  
Rahmad Akbar ◽  
Robert Frank ◽  
Milena Pavlović ◽  
Michael Widrich ◽  
...  
Keyword(s):  
Machine Learning ◽  
In Silico ◽  
Prediction Accuracy ◽  
Large Scale ◽  
Structural Information ◽  
Antigen Binding ◽  
Antibody Specificity ◽  
Binding Prediction ◽  
Information Encoding ◽  
Prediction Problems

Machine learning (ML) is a key technology to enable accurate prediction of antibody-antigen binding, a prerequisite for in silico vaccine and antibody design. Two orthogonal problems hinder the current application of ML to antibody-specificity prediction and the benchmarking thereof: (i) The lack of a unified formalized mapping of immunological antibody specificity prediction problems into ML notation and (ii) the unavailability of large-scale training datasets. Here, we developed the Absolut! software suite that allows the parameter-based unconstrained generation of synthetic lattice-based 3D-antibody-antigen binding structures with ground-truth access to conformational paratope, epitope, and affinity. We show that Absolut!-generated datasets recapitulate critical biological sequence and structural features that render antibody-antigen binding prediction challenging. To demonstrate the immediate, high-throughput, and large-scale applicability of Absolut!, we have created an online database of 1 billion antibody-antigen structures, the extension of which is only constrained by moderate computational resources. We translated immunological antibody specificity prediction problems into ML tasks and used our database to investigate paratope-epitope binding prediction accuracy as a function of structural information encoding, dataset size, and ML method, which is unfeasible with existing experimental data. Furthermore, we found that in silico investigated conditions, predicted to increase antibody specificity prediction accuracy, align with and extend conclusions drawn from experimental antibody-antigen structural data. In summary, the Absolut! framework enables the development and benchmarking of ML strategies for biotherapeutics discovery and design.

scholarly journals Editorial: Linking experimental and computational connectomics

2019 ◽  
Vol 3 (4) ◽  
pp. 902-904
Author(s):  
Alexander Peyser ◽  
Sandra Diaz Pier ◽  
Wouter Klijn ◽  
Abigail Morrison ◽  
Jochen Triesch
Keyword(s):  
High Performance Computing ◽  
In Silico ◽  
High Performance ◽  
Large Scale ◽  
Generative Models ◽  
Anatomical Structure ◽  
Global Function ◽  
Theoretical Neuroscience ◽  
New Generation ◽  
Performance Computing

Large-scale in silico experimentation depends on the generation of connectomes beyond available anatomical structure. We suggest that linking research across the fields of experimental connectomics, theoretical neuroscience, and high-performance computing can enable a new generation of models bridging the gap between biophysical detail and global function. This Focus Feature on ”Linking Experimental and Computational Connectomics” aims to bring together some examples from these domains as a step toward the development of more comprehensive generative models of multiscale connectomes.

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