scholarly journals Developing Software for a Scientific Community

Author(s):  
Judith Segal ◽  
Chris Morris

There are significant challenges in developing scientific software for a broad community. In this chapter, we discuss how these challenges are somewhat different both from those encountered when a scientist end-user developer develops software to address a very specific scientific problem of his/her own, and from those encountered in many commercial developments. However, many developers of scientific community software are steeped in the culture of either scientific end-user or commercial development. As we shall discuss herein, neither background provides sufficient experience so as to meet the challenges of developing software for a scientific community. We make various proposals as to which development approaches, methods, techniques and tools might be useful in this context, and just as importantly, which might not.

Author(s):  
Maria Gilda Pimentel Esteves ◽  
Jano Moreira de Souza ◽  
Alexandre Prestes Uchoa ◽  
Carla Viana Pereira ◽  
Marcio Antelio

This chapter focuses on how, by “activating” the citizen's engagement in the research process, the scientific community has a smart way to benefit from the wisdom of the “crowd”. There are countless success stories in which citizens participate, contributing with their knowledge, cognitive capacity, creativity, opinion, and skills. However, for many scientists, the lack of familiarity with the particular nature of citizen participation, which is usually anonymous and volatile, turns into a barrier for its adoption. This chapter presents a problem-based typology for citizen-science projects that aims to help scientists to choose the best strategy for engaging and counting on citizen participation based on the scientific problem at hand; and some examples are included. Moreover, the chapter discusses the main challenges for researchers who intend to start involving the citizens in order to solve their specific scientific needs.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Julia Koehler Leman ◽  
Sergey Lyskov ◽  
Steven M. Lewis ◽  
Jared Adolf-Bryfogle ◽  
Rebecca F. Alford ◽  
...  

AbstractEach year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.


2020 ◽  
Vol 16 (11) ◽  
pp. e1008390
Author(s):  
Joseph D. Romano ◽  
Jason H. Moore

Papers describing software are an important part of computational fields of scientific research. These “software papers” are unique in a number of ways, and they require special consideration to improve their impact on the scientific community and their efficacy at conveying important information. Here, we discuss 10 specific rules for writing software papers, covering some of the different scenarios and publication types that might be encountered, and important questions from which all computational researchers would benefit by asking along the way.


2021 ◽  
Vol 9 ◽  
Author(s):  
A. Palomo ◽  
O. Maltseva ◽  
I. Garcia-Lodeiro ◽  
A. Fernández-Jiménez

This review undertakes rigorous analysis of much of the copious literature available to the scientific community on the use of alkali-activated binders (AABs) in construction. The authors’ main intention is to categorically refute arguments of that part of the scientific community underestimating or even dismissing the actual potential of AABs as alternatives to Portland cement (PC). The main premise invoked in support of those arguments is a presumed lack of material resources for precursors that would make AAB industrial-scale production unfeasible anywhere on the planet (a substantial number of scientific papers show that the raw materials required for AAB manufacture are in abundance worldwide). The review also analyses the role of alkaline activators in the chemistry of AABs; it is important to clarify and highlight that alkaline activators are not, by any means, confined to the two synthetic products (caustic soda and waterglass) mostly employed by researchers; other sustainable and efficient products are widely available. Finally, the review deals with the versatility of AAB production processes. The technologies required for the large scale manufacturing of AABs are mostly already in place in PC factories; actually no huge investment is required to transform a PC plant in a AAB factory; and quality and compositional uniformity of Alkaline Cements (binders produced through an industrial process) would be guaranteed. The last conclusions extracted from this review-paper are related with: i) the low carbon footprint of one-part AABs and ii) the urgent need of exploring standardization formulas allowing the commercial development of (sustainable) binders different from PC.


Author(s):  
Julia Koehler Leman ◽  
Sergey Lyskov ◽  
Steven Lewis ◽  
Jared Adolf-Bryfogle ◽  
Rebecca F. Alford ◽  
...  

AbstractEach year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.


Crowdsourcing ◽  
2019 ◽  
pp. 929-951
Author(s):  
Maria Gilda Pimentel Esteves ◽  
Jano Moreira de Souza ◽  
Alexandre Prestes Uchoa ◽  
Carla Viana Pereira ◽  
Marcio Antelio

This chapter focuses on how, by “activating” the citizen's engagement in the research process, the scientific community has a smart way to benefit from the wisdom of the “crowd”. There are countless success stories in which citizens participate, contributing with their knowledge, cognitive capacity, creativity, opinion, and skills. However, for many scientists, the lack of familiarity with the particular nature of citizen participation, which is usually anonymous and volatile, turns into a barrier for its adoption. This chapter presents a problem-based typology for citizen-science projects that aims to help scientists to choose the best strategy for engaging and counting on citizen participation based on the scientific problem at hand; and some examples are included. Moreover, the chapter discusses the main challenges for researchers who intend to start involving the citizens in order to solve their specific scientific needs.


Author(s):  
John R. Porter

New ceramic fibers, currently in various stages of commercial development, have been consolidated in intermetallic matrices such as γ-TiAl and FeAl. Fiber types include SiC, TiB2 and polycrystalline and single crystal Al2O3. This work required the development of techniques to characterize the thermochemical stability of these fibers in different matrices.SEM/EDS elemental mapping was used for this work. To obtain qualitative compositional/spatial information, the best realistically achievable counting statistics were required. We established that 128 × 128 maps, acquired with a 20 KeV accelerating voltage, 3 sec. live time per pixel (total mapping time, 18 h) and with beam current adjusted to give 30% dead time, provided adequate image quality at a magnification of 800X. The maps were acquired, with backgrounds subtracted, using a Noran TN 5500 EDS system. The images and maps were transferred to a Macintosh and converted into TIFF files using either TIFF Maker, or TNtolMAGE, a Microsoft QuickBASIC program developed at the Science Center. From TIFF files, images and maps were opened in either NIH Image or Adobe Photoshop for processing and analysis and printed from Microsoft Powerpoint on a Kodak XL7700 dye transfer image printer.


Author(s):  
W.W. Adams ◽  
S. J. Krause

Rigid-rod polymers such as PBO, poly(paraphenylene benzobisoxazole), Figure 1a, are now in commercial development for use as high-performance fibers and for reinforcement at the molecular level in molecular composites. Spinning of liquid crystalline polyphosphoric acid solutions of PBO, followed by washing, drying, and tension heat treatment produces fibers which have the following properties: density of 1.59 g/cm3; tensile strength of 820 kpsi; tensile modulus of 52 Mpsi; compressive strength of 50 kpsi; they are electrically insulating; they do not absorb moisture; and they are insensitive to radiation, including ultraviolet. Since the chain modulus of PBO is estimated to be 730 GPa, the high stiffness also affords the opportunity to reinforce a flexible coil polymer at the molecular level, in analogy to a chopped fiber reinforced composite. The objectives of the molecular composite concept are to eliminate the thermal expansion coefficient mismatch between the fiber and the matrix, as occurs in conventional composites, to eliminate the interface between the fiber and the matrix, and, hopefully, to obtain synergistic effects from the exceptional stiffness of the rigid-rod molecule. These expectations have been confirmed in the case of blending rigid-rod PBZT, poly(paraphenylene benzobisthiazole), Figure 1b, with stiff-chain ABPBI, poly 2,5(6) benzimidazole, Fig. 1c A film with 30% PBZT/70% ABPBI had tensile strength 190 kpsi and tensile modulus of 13 Mpsi when solution spun from a 3% methane sulfonic acid solution into a film. The modulus, as predicted by rule of mixtures, for a film with this composition and with planar isotropic orientation, should be 16 Mpsi. The experimental value is 80% of the theoretical value indicating that the concept of a molecular composite is valid.


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