scholarly journals OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features

2018 ◽  
Author(s):  
Mark A. Hallen ◽  
Jeffrey W. Martin ◽  
Adegoke Ojewole ◽  
Jonathan D. Jou ◽  
Anna U. Lowegard ◽  
...  
Keyword(s):  
Protein Binding ◽  
Open Source ◽  
Protein Design ◽  
Open Source Software ◽  
Ease Of Use ◽  
Biophysical Modeling ◽  
Order Of Magnitude ◽  
Design Software ◽  
Protein Redesign ◽  
New Algorithms

We present OSPREY 3.0, a new and greatly improved release of the OSPREY protein design software. OSPREY 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than previous versions of OSPREY when running the same algorithms on the same hardware. Moreover, OSPREY 3.0 includes several new algorithms, which introduce substantial speedups as well as improved biophysical modeling. It also includes GPU support, which provides an additional speedup of over an order of magnitude. Like previous versions of OSPREY, OSPREY 3.0 offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design and model conformational entropy. Finally, we show here empirically that OSPREY 3.0 accurately predicts the effect of mutations on protein-protein binding. OSPREY 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and open-source software.

scholarly journals Positive multistate protein design

2019 ◽  
Vol 36 (1) ◽  
pp. 122-130
Author(s):  
Jelena Vucinic ◽  
David Simoncini ◽  
Manon Ruffini ◽  
Sophie Barbe ◽  
Thomas Schiex
Keyword(s):  
Protein Design ◽  
Critical Role ◽  
Average Energy ◽  
Computational Design ◽  
Amino Acid Sequences ◽  
Supplementary Information ◽  
Backbone Flexibility ◽  
Identify Amino Acid ◽  
Design Software ◽  
Protein Redesign

Abstract Motivation Structure-based computational protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to identify amino acid sequences that fold into a target structure and ultimately perform a desired function. The usual approach considers a single rigid backbone as a target, which ignores backbone flexibility. Multistate design (MSD) allows instead to consider several backbone states simultaneously, defining challenging computational problems. Results We introduce efficient reductions of positive MSD problems to Cost Function Networks with two different fitness definitions and implement them in the Pompd (Positive Multistate Protein design) software. Pompd is able to identify guaranteed optimal sequences of positive multistate full protein redesign problems and exhaustively enumerate suboptimal sequences close to the MSD optimum. Applied to nuclear magnetic resonance and back-rubbed X-ray structures, we observe that the average energy fitness provides the best sequence recovery. Our method outperforms state-of-the-art guaranteed computational design approaches by orders of magnitudes and can solve MSD problems with sizes previously unreachable with guaranteed algorithms. Availability and implementation https://forgemia.inra.fr/thomas.schiex/pompd as documented Open Source. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics

Metabolites ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 28 ◽  
Author(s):  
Álvaro Fernández-Ochoa ◽  
Rosa Quirantes-Piné ◽  
Isabel Borrás-Linares ◽  
María de la Luz Cádiz-Gurrea ◽  
Marta E. Alarcón Riquelme ◽  
...  
Keyword(s):  
Case Report ◽  
Data Quality ◽  
Open Source ◽  
Open Source Software ◽  
Ease Of Use ◽  
Plasma Samples ◽  
Batch Effects ◽  
Multivariate Models ◽  
Metabolomic Study

Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report aims to compare two specific methodologies, Agilent Profinder vs. R pipeline, for a metabolomic study with a large number of samples. Specifically, 369 plasma samples were analyzed by HPLC-ESI-QTOF-MS. The collected data were pre-processed by both methodologies and later evaluated by several parameters (number of peaks, degree of missingness, quality of the peaks, degree of misalignments, and robustness in multivariate models). The vendor software was characterized by ease of use, friendly interface and good quality of the graphs. The open source methodology could more effectively correct the drifts due to between and within batch effects. In addition, the evaluated statistical methods achieved better classification results with higher parsimony for the open source methodology, indicating higher data quality. Although both methodologies have strengths and weaknesses, the open source methodology seems to be more appropriate for studies with a large number of samples mainly due to its higher capacity and versatility that allows combining different packages, functions, and methods in a single environment.

3D Virtual Planning for Rhinoplasty Using a Free Add-On for Open-Source Software

2021 ◽  
Author(s):  
Davi S Sobral ◽  
Daniele W Duarte ◽  
Rodrigo F V Dornelles ◽  
Cícero A C Moraes
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Low Cost ◽  
Healthcare Providers ◽  
Three Dimensional ◽  
Positive Outcomes ◽  
Virtual Planning ◽  
Good Communication ◽  
Design Software ◽  
Free Open Source

Abstract Background Rhinoplasty is one of the most frequent aesthetic surgeries; the procedure can be challenging for inexperienced surgeons, and positive outcomes depend on good communication with the patient, proper planning, and precise execution. Three-dimensional (3D) technology has emerged to address these issues, but specific software for 3D planning tends to be expensive. Objectives This study presents a simple, low-cost method for 3D simulation to plan rhinoplasty. Methods This preliminary report describes 3D rhinoplasty planning in a series of 3 cases employing free software and an add-on especially developed for rhinoplasty (Blender and RhinOnBlender, respectively). The photogrammetry protocol, which can be performed easily with a smartphone, is described in detail along with all the steps in 3D planning. Results The software and add-on automated the process, making the tool environment accessible to surgeons who are not familiar with graphic design software. The surgeries were uneventful in all cases, and the patients were satisfied with the outcomes. Conclusions 3D graphic technology has provided significant advances in health research, improvement, and teaching for surgeons and communication between surgeons and patients. Free open-source software and add-ons are excellent options that offer proven utility, affordability, and ease of utilization to healthcare providers.

scholarly journals The Challenges of Open Source Software Alternatives

2021 ◽  
Vol 251 ◽  
pp. 01003
Author(s):  
Aristofanis Chionis-Koufakos ◽  
Maria Dimou ◽  
Michal Kolodziejski
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Business Processes ◽  
Personal Data ◽  
Ease Of Use ◽  
User Requirements ◽  
Web Based ◽  
Software Application ◽  
Operational Quality

Developing an Open Source Software application is a challenge. Mainly because there are commercial alternatives that have an army of expert developers behind them, experienced supporters and wellestablished business processes in their development and promotion. Nevertheless, web-based applications, that securely handle the users’ personal data are an area of freedom and ease of use, features that make such applications very attractive. The “ease-of-use” part is very hard to achieve, for the developers and the end-users. Dependencies change often in OSS packages, so the fear that something breaks is always around the corner. If the application looks attractive, additional user requirements fall like rain. This poses a problem of continuity, maintenance and operational quality of the packages. In this paper and presentation we shall share our experience in building such a tool, using https://cern.ch/slides, as a showcase and a learning exercise. We shall describe what was available, what was missing, how it was put together, how much effort it took, and what was achieved.

Yacht Design Software 2.0: The Open Source Movement

2009 ◽  
Author(s):  
Mathew Bird ◽  
William F. Cook ◽  
George S. Hazen ◽  
Britton Ward
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Essential Elements ◽  
Current State ◽  
Custom Software ◽  
External Contribution ◽  
Closed Systems ◽  
Design Software ◽  
Private Actors ◽  
Closed Environment

This paper is a survey of the current state of the art of open source software for yacht design applications. Yacht design and design tools we use have undergone numerous transformations in recent decades, the most notable being the introduction of the personal computer. Since the advent of the PC, yacht designers have been forced to create their own programs from scratch or choosing from relatively few off-the-shelf programs. Commercial software has been characterized by high expense, closed systems, and limited interoperability between applications that are difficult to fully customize or use in a collaborative manner. A lot of sneaker-netting and custom conversion code is often required. For the last several years, users in many industries have been given a new option of joining the “open source movement,” where software and the underlying code is made available for users to download, modify, improve and again make available to others. With open source, the isolated approach to custom software development can be replaced with a broad base of core capability that can be extended and shared with the larger community. Industry players collaborate on the essential elements of tools for our profession - as the saying goes, "A rising tide will lift all boats." There is still plenty of room for individuals or companies to differentiate themselves by how they use the tools and by their niche areas of expertise or experience, but the return on investing in an 'open source' set of common tools is potentially greater than its cost. In doing so, software tools are developed and improved in a collaborative manner, resulting in shorter development time and applications that are more powerful, robust and interoperable for all users. Although working in a closed environment may feel safe and secure to private actors, the lack of adequate peer review and external contribution leads to situation specific myopia. In this paper, we will survey available open source tools both general and yacht design specific that can be used, present some suggestions on integrating them into the design process and explore how the industry can improve these tools in the future.

scholarly journals Predicting Students’ Behavioral Intention to Use Open Source Software: A Combined View of the Technology Acceptance Model and Self-Determination Theory

2020 ◽  
Vol 10 (8) ◽  
pp. 2711 ◽  
Author(s):  
F. José Racero ◽  
Salvador Bueno ◽  
M. Dolores Gallego
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Behavioral Intention ◽  
Self Determination Theory ◽  
Ease Of Use ◽  
Perceived Usefulness ◽  
Self Determination ◽  
Intention To Use ◽  
Acceptance Model ◽  
Behavioral Intention To Use

This study focuses on students’ behavioral intention to use Open Source Software (OSS). The article examines how students, who were trained in OSS, are motivated to continue using it. A conceptual model based on Self-Determination Theory and the Technological Acceptance Model (TAM) was defined in order to test the behavioral intention to use OSS, comprising six constructs: (1) autonomy, (2) competence, (3) relatedness, (4) perceived ease of use, (5) perceived usefulness and (6) behavioral intention to use. A survey was designed for data collection. The participants were recent secondary school graduates, and all of them had received mandatory OSS training. A total of 352 valid responses were used to test the proposed structural model, which was performed using the Lisrel software. The results clearly confirmed the positive influence of the intrinsic motivations; autonomy and relatedness, to improve perceptions regarding the usefulness and ease of use of OSS, and; therefore, on behavioral intention to use OSS. In addition, the implications and limitations of this study are considered.

A Virtual Reality Environment to Visualize Three-Dimensional Patient-Specific Models by a Mobile Head-Mounted Display

2019 ◽  
Vol 26 (3) ◽  
pp. 359-370 ◽  
Author(s):  
Maurizio Vertemati ◽  
Simone Cassin ◽  
Francesco Rizzetto ◽  
Angelo Vanzulli ◽  
Marco Elli ◽  
...  
Keyword(s):  
Virtual Reality ◽  
Open Source ◽  
Open Source Software ◽  
Preoperative Planning ◽  
Low Cost ◽  
Anatomical Variations ◽  
Ease Of Use ◽  
Patient Specific ◽  
Cross Sectional ◽  
Head Mounted Display

Introduction. With the availability of low-cost head-mounted displays (HMDs), virtual reality environments (VREs) are increasingly being used in medicine for teaching and clinical purposes. Our aim was to develop an interactive, user-friendly VRE for tridimensional visualization of patient-specific organs, establishing a workflow to transfer 3-dimensional (3D) models from imaging datasets to our immersive VRE. Materials and Methods. This original VRE model was built using open-source software and a mobile HMD, Samsung Gear VR. For its validation, we enrolled 33 volunteers: morphologists (n = 11), trainee surgeons (n = 15), and expert surgeons (n = 7). They tried our VRE and then filled in an original 5-point Likert-type scale 6-item questionnaire, considering the following parameters: ease of use, anatomy comprehension compared with 2D radiological imaging, explanation of anatomical variations, explanation of surgical procedures, preoperative planning, and experience of gastrointestinal/neurological disorders. Results in the 3 groups were statistically compared using analysis of variance. Results. Using cross-sectional medical imaging, the developed VRE allowed to visualize a 3D patient-specific abdominal scene in 1 hour. Overall, the 6 items were evaluated positively by all groups; only anatomy comprehension was statistically significant different among the 3 groups. Conclusions. Our approach, based on open-source software and mobile hardware, proved to be a valid and well-appreciated system to visualize 3D patient-specific models, paving the way for a potential new tool for teaching and preoperative planning.

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