scholarly journals SurfStamp: 3D Printer Compatible Molecular Surface Representation

2020 ◽  
Author(s):  
Toshiyuki Oda
Keyword(s):  
Open Source ◽  
Source Code ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Surface ◽  
3D Printer ◽  
3D Object ◽  
Link Type ◽  
Surface Models ◽  
Version 2.0

AbstractSurfStamp is an application that is used to generate textures for surface models of proteins. The textures contain information about surface residues and the information is drawn directly on the 3D object of the models. This approach is more intuitive than the labeling functions that most three-dimensional (3D) structure viewers use to show residue information. Therefore, the use of this application enables researchers, readers, or audiences to easily determine which residues are contributing the surface they are focusing on.AvailabilityThe application is provided under the open-source Apache License Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0). The application and source code are available from https://github.com/yamule/SurfStamp-public/releases.

scholarly journals Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

2021 ◽  
Author(s):  
Soohyun Lee ◽  
Carl Vitzthum ◽  
Burak H. Alver ◽  
Peter J. Park
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Source Code ◽  
Three Dimensional ◽  
File Format ◽  
Interaction Data ◽  
Text File ◽  
Storage And Retrieval ◽  
Link Type ◽  
Efficient Storage

AbstractSummaryAs the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.AvailabilityThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/[email protected] or [email protected]

scholarly journals quasitools: A Collection of Tools for Viral Quasispecies Analysis

2019 ◽  
Author(s):  
Eric Marinier ◽  
Eric Enns ◽  
Camy Tran ◽  
Matthew Fogel ◽  
Cole Peters ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Distance ◽  
Open Source ◽  
Source Code ◽  
Viral Quasispecies ◽  
Consensus Sequences ◽  
Link Type ◽  
Version 2.0 ◽  
Amino Acid Variants

AbstractSummaryquasitools is a collection of newly-developed, open-source tools for analyzing viral quasispcies data. The application suite includes tools with the ability to create consensus sequences, call nucleotide, codon, and amino acid variants, calculate the complexity of a quasispecies, and measure the genetic distance between two similar quasispecies. These tools may be run independently or in user-created workflows.AvailabilityThe quasitools suite is a freely available application licensed under the Apache License, Version 2.0. The source code, documentation, and file specifications are available at: https://phac-nml.github.io/quasitools/[email protected]

scholarly journals Effects of Nozzle Die Angle on Extruding Polymethylmethacrylate in Open-Source 3D Printing

2018 ◽  
Vol 15 (2) ◽  
pp. 663-665 ◽  
Author(s):  
Nor Aiman Sukindar ◽  
Mohd Khairol Anuar Mohd Ariffin ◽  
B.T. Hang Tuah Baharudin ◽  
Che Nor Aiza Jaafar ◽  
Mohd Idris Shah Ismail
Keyword(s):  
Finite Element Analysis ◽  
Finite Element ◽  
Pressure Drop ◽  
3D Printing ◽  
Open Source ◽  
Flow Behavior ◽  
Three Dimensional ◽  
3D Printer ◽  
Element Analysis ◽  
Factors Affecting

Open-source 3D printer has been widely used for fabricating three dimensional products. However, this technology has some drawbacks that need to be improved such as accuracy of the finished parts. One of the factors affecting the final product is the ability of the machine to extrude the material consistently, which is related to the flow behavior of the material inside the liquefier. This paper observes the pressure drop along the liquefier by manipulating the nozzle die angle from 80° to 170° using finite element analysis (FEA) for polymethylmethacrylate (PMMA) material. When the pressure drop along the liquefier is varied, the printed product also varies, thus providing less accuracy in the finished parts. Based on the FEA, it was found that 130° was the optimum die angle (convergent angle) for extruding PMMA material using open-source 3D printing.

scholarly journals Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images

2021 ◽  
Vol 8 ◽  
Author(s):  
Bhaskar Dasgupta ◽  
Osamu Miyashita ◽  
Takayuki Uchihashi ◽  
Florence Tama
Keyword(s):  
Atomic Force Microscopy ◽  
Computational Modeling ◽  
High Speed ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Computational Method ◽  
Molecular Surface ◽  
Force Microscopy ◽  
Atomic Force

ClpB belongs to the cellular disaggretase machinery involved in rescuing misfolded or aggregated proteins during heat or other cellular shocks. The function of this protein relies on the interconversion between different conformations in its native condition. A recent high-speed-atomic-force-microscopy (HS-AFM) experiment on ClpB from Thermus thermophilus shows four predominant conformational classes, namely, open, closed, spiral, and half-spiral. Analyses of AFM images provide only partial structural information regarding the molecular surface, and thus computational modeling of three-dimensional (3D) structures of these conformations should help interpret dynamical events related to ClpB functions. In this study, we reconstruct 3D models of ClpB from HS-AFM images in different conformational classes. We have applied our recently developed computational method based on a low-resolution representation of 3D structure using a Gaussian mixture model, combined with a Monte-Carlo sampling algorithm to optimize the agreement with target AFM images. After conformational sampling, we obtained models that reflect conformational variety embedded within the AFM images. From these reconstructed 3D models, we described, in terms of relative domain arrangement, the different types of ClpB oligomeric conformations observed by HS-AFM experiments. In particular, we highlighted the slippage of the monomeric components around the seam. This study demonstrates that such details of information, necessary for annotating the different conformational states involved in the ClpB function, can be obtained by combining HS-AFM images, even with limited resolution, and computational modeling.

A Parallel Multiple Layer Cryolithography Device for the Manufacture of Biological Material for Tissue Engineering

2019 ◽  
Vol 13 (3) ◽  
Author(s):  
Gideon Ukpai ◽  
Joseph Sahyoun ◽  
Robert Stuart ◽  
Sky Wang ◽  
Zichen Xiao ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Additive Manufacturing ◽  
3D Printing ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Object ◽  
New Device ◽  
Biological Matter ◽  
Simple Product ◽  
Printing Processes

While three-dimensional (3D) printing of biological matter is of increasing interest, current linear 3D printing processes lack the efficiency at scale required to mass manufacture products made of biological matter. This paper introduces a device for a newly developed parallel additive manufacturing technology for production of 3D objects, which addresses the need for faster, industrial scale additive manufacturing methods. The technology uses multilayer cryolithography (MLCL) to make biological products faster and in larger quantities by simultaneously printing two-dimensional (2D) layers in parallel and assembling the layers into a 3D structure at an assembly site, instead of sequentially and linearly assembling a 3D object from individual elements as in conventional 3D printing. The technique uses freezing to bind the 2D layers together into a 3D object. This paper describes the basic principles of MLCL and demonstrates the technology with a new device used to manufacture a very simple product that could be used for tissue engineering, as an example. An evaluation of the interlayer bonding shows that a continuous and coherent structure can be made from the assembly of distinct layers using MLCL.

scholarly journals Matchathon: A guide to student-faculty connections in PhD programs

2020 ◽  
Author(s):  
Haley Amemiya ◽  
Zena Lapp ◽  
Cathy Smith ◽  
Margaret Durdan ◽  
Michelle DiMondo ◽  
...  
Keyword(s):  
Open Source ◽  
Source Code ◽  
Faculty Members ◽  
Retention Rates ◽  
Link Type ◽  
Shiny App ◽  
R Shiny ◽  
Web App ◽  
Phd Programs ◽  
The Web

AbstractRelevant and impactful mentors are essential to a graduate student’s career. Finding mentors can be challenging in umbrella programs with hundreds of faculty members. To foster connections between potential mentors and students with similar research interests, we created a Matchathon event, which has successfully enabled students to find mentors. We developed an easy-to-use R Shiny app (https://github.com/UM-OGPS/matchathon/) to facilitate matching and organizing the event that can be used at any institution. It is our hope that this resource will improve the environment and retention rates for students in the academy.The open source app is publicly available on the web (app: https://UM-OGPS.shinyapps.io/matchathon/; source code: https://github.com/UM-OGPS/matchathon/).

scholarly journals A RESTful API to serve BAM file with OAuth2 compatible authorization

2017 ◽  
Author(s):  
Julien Delafontaine ◽  
Sylvain Pradervand
Keyword(s):  
Open Source ◽  
Source Code ◽  
Variant Calling ◽  
Use Case ◽  
Web Interface ◽  
Sensitive Data ◽  
Link Type ◽  
Restful Service

AbstractSummaryBam-server is an open-source RESTful service to query slices of BAM files securely and manage their user accesses. A typical use case is the visualization of local read alignments in a web interface for variant calling diagnostic, without exposing sensitive data to unauthorized users through the network, and without moving the original - heavy - file. Bam-server follows the standard implementation of a protected resource server in the context of a typical token-based authorization protocol, supporting HMAC- and RSA-hashed signatures from an authorization server of choice.AvailabilityThe source code is available at https://github.com/chuv-ssrc/bam-server-scala, and a complete documentation can be found at http://bam-server-scala.readthedocs.io/en/latest/[email protected]

scholarly journals Edlib: a C/C++ library for fast, exact sequence alignment using edit distance

2016 ◽  
Author(s):  
Martin Šošić ◽  
Mile Šikić
Keyword(s):  
Exact Sequence ◽  
Open Source ◽  
Sequence Alignment ◽  
Test Data ◽  
Edit Distance ◽  
Source Code ◽  
Memory Usage ◽  
Pairwise Sequence Alignment ◽  
Link Type ◽  
Bioinformatics Tools

AbstractWe present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be a cornerstone for many future bioinformatics tools.Source code, installation instructions and test data are freely available for download at https://github.com/Martinsos/edlib, implemented in C/C++ and supported on Linux, MS Windows, and Mac OS.Contact:[email protected]

scholarly journals ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

2019 ◽  
Author(s):  
Egor Dolzhenko ◽  
Viraj Deshpande ◽  
Felix Schlesinger ◽  
Peter Krusche ◽  
Roman Petrovski ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Broad Class ◽  
Source Code ◽  
Computational Method ◽  
Dna Repeats ◽  
Link Type ◽  
Sequence Graph ◽  
Version 2.0 ◽  
Short Tandem

SummaryWe describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci.Availability and implementationExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/[email protected]

scholarly journals Three-dimensional semi-automated volumetric assessment of the pulp space of teeth following regenerative dental procedures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Heeresh Shetty ◽  
Shishir Shetty ◽  
Adesh Kakade ◽  
Aditya Shetty ◽  
Mohmed Isaqali Karobari ◽  
...  
Keyword(s):  
Medical Imaging ◽  
Open Source ◽  
Three Dimensional ◽  
Volume Estimation ◽  
Permanent Teeth ◽  
3D Slicer ◽  
Link Type ◽  
Volumetric Assessment ◽  
Critical Measure ◽  
Significant Difference

AbstractThe volumetric change that occurs in the pulp space over time represents a critical measure when it comes to determining the secondary outcomes of regenerative endodontic procedures (REPs). However, to date, only a few studies have investigated the accuracy of the available domain-specialized medical imaging tools with regard to three-dimensional (3D) volumetric assessment. This study sought to compare the accuracy of two different artificial intelligence-based medical imaging programs namely OsiriX MD (v 9.0, Pixmeo SARL, Bernex Switzerland, https://www.osirix-viewer.com) and 3D Slicer (http://www.slicer.org), in terms of estimating the volume of the pulp space following a REP. An Invitro assessment was performed to check the reliability and sensitivity of the two medical imaging programs in use. For the subsequent clinical application, pre- and post-procedure cone beam computed tomography scans of 35 immature permanent teeth with necrotic pulp and periradicular pathosis that had been treated with a cell-homing concept-based REP were processed using the two biomedical DICOM software programs (OsiriX MD and 3D Slicer). The volumetric changes in the teeth’s pulp spaces were assessed using semi-automated techniques in both programs. The data were statistically analyzed using t-tests and paired t-tests (P = 0.05). The pulp space volumes measured using both programs revealed a statistically significant decrease in the pulp space volume following the REP (P < 0.05), with no significant difference being found between the two programs (P > 0.05). The mean decreases in the pulp space volumes measured using OsiriX MD and 3D Slicer were 25.06% ± 19.45% and 26.10% ± 18.90%, respectively. The open-source software (3D Slicer) was found to be as accurate as the commercially available software with regard to the volumetric assessment of the post-REP pulp space. This study was the first to demonstrate the step-by-step application of 3D Slicer, a user-friendly and easily accessible open-source multiplatform software program for the segmentation and volume estimation of the pulp spaces of teeth treated with REPs.

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