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检索条件"主题词=Programming language"

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Reconstruction of Genome-Scale Metabolic Model for

Reconstruction of Genome-Scale Metabolic Model for

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作者： Francisco Zorrilla Eduard J. Kerkhoven

Genome-scale metabolic models (GEMs) provide a useful framework for modeling the metabolism of microorganisms. While the applications of GEMs are wide and far reaching, the reconstruction and continuous curation of such models can be perceived as a tedious and time-consuming task. Using RAVEN, a MATLAB-based toolbox designed to facilitate the reconstruction analysis of metabolic networks, this protocol practically demonstrates how researchers can create their own GEMs using a homology-based approach. To provide a complete example, a draft GEM for the industrially relevant yeast Hansenula polymorpha is reconstructed. less

关键词： programming language Pichia Saccharomyces cerevisiae Metabolism Genome-scale model Constraint-based model

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Analysis of Transcriptomic Data Generated from Drug-Treated Cancer Cell Line

Analysis of Transcriptomic Data Generated from Drug-Treated ...

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作者： Swarnima Kushwaha Sudeshna Mukherjee Rajdeep Chowdhury Shibasish Chowdhury

Resistance to chemotherapy is one major obstacle in current cancer treatment. Therefore, understanding the molecular basis of the acquisition of resistance is vital for the design and development of appropriate cancer therapy. Importantly, acquisition of resistance is not a single-step process, and the molecular signature of cells dynamically changes during this process. With the advent of next-generation omic technologies, today one can precisely map the molecular alterations not only in a population of tumor cells but also at the single-cell level as they attain chemo-resistance. In this chapter, we describe a detailed transcriptomic pipeline following next-generation sequencing for mapping alteration in expression during the process of attainment of resistance. We provide comprehensive information on the process to (1) track the differential expression of transcripts, (2) understand the gene ontology functions, (3) filter out candidate key genes, (4) identify the pathways regulated by them, and (5) generate a map of their probable interactions. We assume that our analytical method will be useful for research in this direction. less

关键词： RNA-seq RNA Extraction mRNA sequencing Data analysis Gel Electrophoresis Deep Sequencing High-Throughput Sequencing TopHat Bowtie programming language Cufflinks Gene Expression Analysis Cuffdiff Cytoscape Data Visualization Tools Cell And Tissue Culture Cancer Chemotherapy Drug resistance

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High-Throughput Screening Assay Profiling for Large Chemical Databases

High-Throughput Screening Assay Profiling for Large Chemical...

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作者： Daniel P. Russo Hao Zhu

High-throughput screening (HTS) techniques are increasingly being adopted by a variety of fields of toxicology. Notably, large-scale research efforts from government, industrial, and academic laboratories are screening millions of chemicals against a variety of biomolecular targets, producing an enormous amount of publicly available HTS assay data. These HTS assay data provide toxicologists important information on how chemicals interact with different biomolecular targets and provide illustrations of potential toxicity mechanisms. Open public data repositories, such as the National Institutes of Health’s PubChem (http://*** ), were established to accept, store, and share HTS data. Through the PubChem website, users can rapidly obtain the PubChem assay results for compounds by using different chemical identifiers (including SMILES, InChIKey, IUPAC names, etc.). However, obtaining these data in a user-friendly format suitable for modeling and other informatics analysis (e.g., gathering PubChem data for hundreds or thousands of chemicals in a modeling friendly format) directly through the PubChem web portal is not feasible. This chapter aims to introduce two approaches to obtain the HTS assay results for large datasets of compounds from the PubChem portal. First, programmatic access via PubChem’s PUG-REST web service using the Python programming language will be described. Second, most users, who lack programming skills, can directly obtain PubChem data for a large set of compounds by using the freely available Chemical In vitro–In vivo Profiling (CIIPro) portal (http://*** ). less

关键词： High-throughput Screening Python programming language PubChem Biological data In vitro profiling CIIPro

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Using GenBank and SRA

Using GenBank and SRA

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作者： Eric W. Sayers Chris O’Sullivan Ilene Karsch-Mizrachi

GenBank® and the Sequence Read Archive (SRA) are comprehensive databases of publicly available DNA sequences. GenBank contains data for 480,000 named organisms, more than 176,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. SRA contains reads from next-generation sequencing studies from over 110,000 species. Daily data exchange with the European Nucleotide Archive (ENA) in Europe and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage for both databases. GenBank and SRA data are accessible through the NCBI Entrez retrieval system that integrates these data with other data at NCBI, such as genomes, taxonomy, and the biomedical literature. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Usage scenarios for both GenBank and SRA ranging from local and cloud analyses to online analyses supported by the NCBI web-based tools are discussed. Both GenBank and SRA, along with their related retrieval and analysis services, are available from the NCBI homepage at *** . less

关键词： Genome Assembly High-Throughput Sequencing Statistical Calculation GenBank Genome Sequencing programming language Zea mays Nicotiana tabacum Arabidopsis thaliana Oryza sativa Japonica Group Populus trichocarpa Solanum lycopersicum Triticum aestivum Allium Glycine max Pisum sativum BLAST DNA sequence SRA NCBI

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Analysis of Molecular Dynamics Simulations of Protein Folding

Analysis of Molecular Dynamics Simulations of Protein Foldin...

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作者： Robert B. Best

Unbiased molecular dynamics simulations of proteins can now capture spontaneous folding events. This provides a wealth of data reflecting information on folding mechanism, but raises the challenge of interpreting it in a meaningful way. Here, I describe how such simulations can be used to identify reactive states and reaction coordinates for describing folding, and how folding dynamics can be captured by projection onto those coordinates. Methods are described for quantifying the interactions important for defining the folding mechanism, and for comparison of simulations with experimental mechanistic probes, such as ϕ-values. less

关键词： Molecular Dynamics Simulation Python programming language Committor Markov state model Reaction coordinate Transition path Native contacts Bayesian criterion

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Cell-Free Biosensors and AI Artificial intelligence (AI) Integration

Cell-Free Biosensors and AI Artificial intelligence (AI) Int...

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作者： Paul Soudier Léon Faure Maish Kushwaha Jean-Loup Faulon

Cell-free biosensors hold a great potential as alternatives for traditional analytical chemistry methods providing low-cost low-resource measurement of specific chemicals. However, their large-scale use is limited by the complexity of their development. In this chapter, we present a standard methodology based on computer-aided design (CADComputer-aided design (CAD)) tools that enables fast development of new cell-free biosensors based on target molecule information transduction and reporting through metabolic and genetic layers, respectively. Such systems can then be repurposed to represent complex computational problems, allowing defined multiplex sensing of various inputs and integration of artificial intelligenceArtificial intelligence (AI) in synthetic biological systems. less

关键词： Machine Learning Neural Network Model Artificial Intelligence Biosensor technique Electrophoresis PCR Sanger Sequencing Dialysis Cell And Tissue Culture Plasmid Purification programming language Transcription factors Metabolite biosensors CAD Perceptron

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Agent-Based Modeling of Complex Molecular Systems

Agent-Based Modeling of Complex Molecular Systems

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作者： Mike Holcombe Eva Qwarnstrom

The seamless integration of laboratory experiments and detailed computational modeling provides an exciting route to uncovering many new insights into complex biological processes. In particular, the development of agent-based modeling using supercomputers has provided new opportunities for highly detailed, validated simulations that provide the researcher with greater understanding of these processes and new directions for investigation. This chapter examines some of the principles behind the powerful computational framework FLAME and its application in a number of different areas with a more detailed look at a particular signaling example involving the NF-κB cascade. less

关键词： programming language ITASSER Cell And Tissue Culture Cytoskeleton Signal transduction NF-κB IL-1 Computational modeling Agent based modeling FLAME IL1R1 complex Map kinase TILRR

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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

Modeling the Structure, Dynamics, and Transformations of Pro...

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作者： Adam K. Sieradzan Cezary Czaplewski Paweł Krupa Magdalena A. Mozolewska Agnieszka S. Karczyńska Agnieszka G. Lipska Emilia A. Lubecka Ewa Gołaś Tomasz Wirecki Mariusz Makowski Stanisław Ołdziej Adam Liwo

The physics-based united-residue (UNRES) model of proteins (*** ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics and its replica-exchange extensions, UNRES has found a variety of applications, including ab initio and database-assisted protein-structure prediction, simulating protein-folding pathways, exploring protein free-energy landscapes, and solving biological problems. This chapter provides a summary of UNRES and a guide for potential users regarding the application of the UNRES package in a variety of research tasks. less

关键词： Molecular Dynamics Simulation Structure Prediction NMR X-ray Scattering Spectroscopy programming language Protein folding Protein dynamics Coarse graining Protein–structure prediction

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All-optical interrogation of neural circuits in behaving mice

All-optical interrogation of neural circuits in behaving mic...

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作者： Lloyd E. Russell Henry W. Dalgleish Rebecca Nutbrown Oliver M. Gauld Dustin Herrmann Mehmet Fişek Adam M. Packer Michael Häusser

Recent advances combining two-photon calcium imaging and two-photon optogenetics with computer-generated holography now allow us to read and write the activity of large populations of neurons in vivo at cellular resolution and with high temporal resolution. Such ‘all-optical’ techniques enable experimenters to probe the effects of functionally defined neurons on neural circuit function and behavioral output with new levels of precision. This greatly increases flexibility, resolution, targeting specificity and throughput compared with alternative approaches based on electrophysiology and/or one-photon optogenetics and can interrogate larger and more densely labeled populations of neurons than current voltage imaging-based implementations. This protocol describes the experimental workflow for all-optical interrogation experiments in awake, behaving head-fixed mice. We describe modular procedures for the setup and calibration of an all-optical system (~3 h), the preparation of an indicator and opsin-expressing and task-performing animal (~3–6 weeks), the characterization of functional and photostimulation responses (~2 h per field of view) and the design and implementation of an all-optical experiment (achievable within the timescale of a normal behavioral experiment; ~3–5 h per field of view). We discuss optimizations for efficiently selecting and targeting neuronal ensembles for photostimulation sequences, as well as generating photostimulation response maps from the imaging data that can be used to examine the impact of photostimulation on the local circuit. We demonstrate the utility of this strategy in three brain areas by using different experimental setups. This approach can in principle be adapted to any brain area to probe functional connectivity in neural circuits and investigate the relationship between neural circuit activity and behavior. less

关键词： Optical Imaging Surgery Two-Photon Calcium Imaging Optogenetics Holography Electrophysiology Two-photon Imaging Chiral Separation Genetic Mapping MATLAB programming language Image Analysis Calcium Imaging Live Cell Imaging In Vivo Imaging Mus musculus Viruses Neuroscience Behavioural methods Neural circuits

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PELDOR Measurements on Nitroxide-Labeled Oligonucleotides

PELDOR Measurements on Nitroxide-Labeled Oligonucleotides

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作者： Tobias Hett Olav Schiemann

In the past decades, pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) has emerged as a powerful tool in biophysical chemistry to study the structure, dynamics, and function of biomolecules like oligonucleotides and proteins. Structural information is obtained from PDS methods in form of a distribution of distances between spin centers. Such spin centers can either be intrinsically present paramagnetic metal ions and organic radicals or may be attached to the biomolecule by means of site-directed spin labeling. The most common PDS experiment for probing interspin distances in the nanometer range is pulsed electron–electron double resonance (PELDOR or DEER). In the protocol presented here, we provide a step-by-step workflow on how to set up a PELDOR experiment on a commercially available pulsed EPR spectrometer, outline the data analysis, and highlight potential pitfalls. We suggest PELDOR measurements on nitroxide-labeled oligonucleotides to study the structure of either RNA-cleaving DNAzymes in complex with their RNA targets or modified DNAzymes with different functions and targets, in which deoxynucleotides are substituted by nitroxide-labeled nucleotides. less

关键词： Spectroscopy Electron Spin Resonance Spectroscopy Two-pulse Electron Spin-echo Envelope Modulation Electron Spin Echo Envelope Modulation Spectroscopy Phase Cycle Rutherford Backscattering Spectroscopy Deep learning MATLAB Data analysis programming language Electron paramagnetic resonance (EPR) Spin label Electron spin resonance (ESR) Double electron–electron resonance (DEER) Pulsed electron–electron double resonance (PELDOR)

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