MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.

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MAYGEN - an Open-Source Chemical Structure Generator for Constitutional Isomers Based on the Orderly Generation Principle

10.26434/chemrxiv.14497959 ◽

2021 ◽

Author(s):

Mehmet Aziz Yirik ◽

Maria Sorokina ◽

Christoph Steinbeck

Keyword(s):

Open Source ◽

Structure Elucidation ◽

Chemical Structure ◽

State Of The Art ◽

The State ◽

Molecular Generator ◽

Structure Generator ◽

Order Of Magnitude ◽

Closed Source

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.

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MAYGEN - an Open-Source Chemical Structure Generator for Constitutional Isomers Based on the Orderly Generation Principle

10.26434/chemrxiv.14497959.v2 ◽

2021 ◽

Author(s):

Mehmet Aziz Yirik ◽

Maria Sorokina ◽

Christoph Steinbeck

Keyword(s):

Open Source ◽

Structure Elucidation ◽

Chemical Structure ◽

State Of The Art ◽

The State ◽

Molecular Generator ◽

Structure Generator ◽

Order Of Magnitude ◽

Closed Source

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.

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Measuring impedance using an open-source instrumentation platform

International Journal of Electrical Engineering Education ◽

10.1177/0020720918761764 ◽

2018 ◽

Vol 55 (2) ◽

pp. 168-185

Author(s):

Urban Burnik ◽

Dejan Križaj ◽

Zumret Topčagić ◽

Marko Meža

Keyword(s):

Open Source ◽

Electrical Impedance ◽

State Of The Art ◽

The State ◽

Impedance Measurements ◽

Engineering Knowledge ◽

Art Analysis ◽

Lcr Meter

The article presents development and design of a precision LCR meter based on an affordable open-source instrumentation platform. The design of the instrument has been performed by an interdisciplinary group of students. A project-based approach has been used in order to make a practical use of engineering knowledge within the group of participants. The results cover all the necessary project results achieved by the participants from the state-of-the art analysis in the domain of LCR meters to dissemination of project results. These may serve as a guide for similar project specifications. Alternatively, the presented results may be used in preparing student assignments in electrical impedance measurements based on affordable hardware.

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Grand challenges in model-driven engineering: an analysis of the state of the research

Software & Systems Modeling ◽

10.1007/s10270-019-00773-6 ◽

2020 ◽

Vol 19 (1) ◽

pp. 5-13 ◽

Cited By ~ 12

Author(s):

Antonio Bucchiarone ◽

Jordi Cabot ◽

Richard F. Paige ◽

Alfonso Pierantonio

Keyword(s):

Open Source ◽

State Of The Art ◽

The State ◽

Model Driven Engineering ◽

Grand Challenges ◽

Model Driven ◽

New Challenges ◽

State Of Practice ◽

State Of Research ◽

Research Initiatives

AbstractIn 2017 and 2018, two events were held—in Marburg, Germany, and San Vigilio di Marebbe, Italy, respectively—focusing on an analysis of the state of research, state of practice, and state of the art in model-driven engineering (MDE). The events brought together experts from industry, academia, and the open-source community to assess what has changed in research in MDE over the last 10 years, what challenges remain, and what new challenges have arisen. This article reports on the results of those meetings, and presents a set of grand challenges that emerged from discussions and synthesis. These challenges could lead to research initiatives for the community going forward.

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Surge - A Fast Open-Source Chemical Graph Generator

10.26434/chemrxiv-2021-gt5lb ◽

2021 ◽

Author(s):

Brendan D. McKay ◽

Mehmet Aziz Yirik ◽

Christoph Steinbeck

Keyword(s):

Open Source ◽

Chemical Structure ◽

Automorphism Groups ◽

Molecular Formula ◽

The Novel ◽

Chemical Graph ◽

Structure Generator ◽

Starting Point ◽

The Given ◽

Input Formula

Chemical structure generators are used in cheminformatics to produce or enumerate virtual molecules based on a set of boundary conditions. The result can then be tested for properties of interest, such as adherence to measured data or for their suitability as drugs. The starting point can be a potentially fuzzy set of fragments or a molecular formula. In the latter case, the generator produces the set of constitutional isomers of the given input formula. Here we present the novel constitutional isomer generator surge based on the canonical generation path method. Surge uses the nauty package to compute automorphism groups of graphs. We outline the working principles of surge and present benchmarking results which show that surge is currently the fastest structure generator. Surge is available under a liberal open-source license.

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Mob Programming: The State of the Art and Three Case Studies of Open Source Software

Agile Methods - Communications in Computer and Information Science ◽

10.1007/978-3-319-73673-0_12 ◽

2018 ◽

pp. 146-160 ◽

Cited By ~ 3

Author(s):

Herez Moise Kattan ◽

Frederico Oliveira ◽

Alfredo Goldman ◽

Joseph William Yoder

Keyword(s):

Open Source ◽

Case Studies ◽

Open Source Software ◽

State Of The Art ◽

The State

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A Review on Bitumen Rejuvenation: Mechanisms, Materials, Methods and Perspectives

Applied Sciences ◽

10.3390/app9204316 ◽

2019 ◽

Vol 9 (20) ◽

pp. 4316 ◽

Cited By ~ 5

Author(s):

Loise ◽

Caputo ◽

Porto ◽

Calandra ◽

Angelico ◽

...

Keyword(s):

Complex Systems ◽

Chemical Structure ◽

Structural Changes ◽

Ad Hoc ◽

State Of The Art ◽

Chemical Interaction ◽

The State ◽

X Ray ◽

X Ray Scattering ◽

Novel Approach

This review aims to explore the state of the knowledge and the state-of-the-art regarding bitumen rejuvenation. In particular, attention was paid to clear things up about the rejuvenator mechanism of action. Frequently, the terms rejuvenator and flux oil, or oil (i.e., softening agent) are used as if they were synonymous. According to our knowledge, these two terms refer to substances producing different modifications to the aged bitumen: they can decrease the viscosity (softening agents), or, in addition to this, restore the original microstructure (real rejuvenators). In order to deal with the argument in its entirety, the bitumen is investigated in terms of chemical structure and microstructural features. Proper investigating tools are, therefore, needed to distinguish the different mechanisms of action of the various types of bitumen, so attention is focused on recent research and the use of different investigation techniques to distinguish between various additives. Methods based on organic synthesis can also be used to prepare ad-hoc rejuvenating molecules with higher performances. The interplay of chemical interaction, structural changes and overall effect of the additive is then presented in terms of the modern concepts of complex systems, which furnishes valid arguments to suggest X-ray scattering and Nuclear Magnetic Resonance relaxometry experiments as vanguard and forefront tools to study bitumen. Far from being a standard review, this work represents a critical analysis of the state-of-the-art taking into account for the molecular basis at the origin of the observed behavior. Furnishing a novel viewpoint for the study of bitumen based on the concepts of the complex systems in physics, it constitutes a novel approach for the study of these systems.

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The history of Blitz/Cray-Blitz/Crafty

ICGA Journal ◽

10.3233/icg-200167 ◽

2020 ◽

Vol 42 (2-3) ◽

pp. 120-131

Author(s):

Robert Hyatt

Keyword(s):

Open Source ◽

State Of The Art ◽

The State ◽

High Performing ◽

Open Source Program ◽

Computer Chess ◽

Source Program ◽

History Of

This article is a series of anecdotes about the development of several programs that advanced the state of the art in computer chess. The best known is Cray Blitz, which won the 1983 and 1986 World Computer Chess Championships. However, in terms of overall impact, perhaps Crafty is the most important. As a high-performing open-source program, it has been used by countless number of researchers and hobbyists to develop computer chess programs for competitions, research, and for fun.

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A Comparison of 3D Collaborative Virtual Learning Environments

International Journal of e-Collaboration ◽

10.4018/jec.2012100102 ◽

2012 ◽

Vol 8 (4) ◽

pp. 8-21 ◽

Cited By ~ 3

Author(s):

Apostolos Mavridis ◽

Andreas Konstantinidis ◽

Thrasyvoulos Tsiatsos

Keyword(s):

Collaborative Learning ◽

Open Source ◽

Learning Environments ◽

Second Life ◽

State Of The Art ◽

Virtual Learning ◽

The State ◽

Virtual Learning Environments ◽

Proprietary Software

This paper focuses on 3D Collaborative Virtual Learning Environments, examining the state of the art in both open source and proprietary software. Issues pertaining to the use of open source Collaborative Virtual Learning Environments are discussed, rationalizing the choice of executing a collaborative learning scenario in Second Life. The scenario is then presented and evaluation results assess the appropriateness of the chosen platform with regards to its technical and pedagogical affordances. Finally, students’ suggestions and reactions towards such a novel didactical approach are discussed.

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