BoneJ2 - refactoring established research software.
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ABSTRACT:
SUBMITTER: Domander R
PROVIDER: S-EPMC8063517 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background and purposeWe aimed to determine the intermethod reproducibility between the commercial software Inbrain (MIDAS IT) and the established research-purpose method FreeSurfer, as well as the effect of MRI resolution and the pathological condition of subjects on their intermethod reproducibility.MethodsThis study included 45 healthy volunteers and 85 patients with mild cognitive impairment (MCI). In 43 of the 85 patients with MCI, three-dimensional, T1-weighted MRI data were obtained at an in-plane resolution of 1.2 mm. The data of the remaining 42 patients with MCI and the healthy volunteers were obtained at an in-plane resolution of 1.0 mm. The within-subject coefficient of variation (CoV), intraclass correlation coefficient (ICC), and effect size were calculated, and means were compared using paired t-tests. The parameters obtained at 1.0-mm and 1.2-mm resolutions in patients with MCI were compared to evaluate the effect of the in-plane resolution on the intermethod reproducibility. The parameters obtained at a 1.0-mm in-plane resolution in patients with MCI and healthy volunteers were used to analyze the effect of subject condition on intermethod reproducibility.ResultsOverall the two methods showed excellent reproducibility across all regions of the brain (CoV=0.5-3.9, ICC=0.93 to >0.99). In the subgroup of healthy volunteers, the intermethod reliability was only good in some regions (frontal, temporal, cingulate, and insular). The intermethod reproducibility was better in the 1.0-mm group than the 1.2-mm group in all regions other than the nucleus accumbens.ConclusionsInbrain and FreeSurfer showed good-to-excellent intermethod reproducibility for volumetric measurements. Nevertheless, some noticeable differences were found based on subject condition, image resolution, and brain region.
| S-EPMC8053534 | biostudies-literature
Project description:Natural biological systems are selected by evolution to continue to exist and evolve. Evolution likely gives rise to complicated systems that are difficult to understand and manipulate. Here, we redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. Our initial design goals were to physically separate and enable unique manipulation of primary genetic elements. Implicit in our design are the hypotheses that overlapping genetic elements are, in aggregate, nonessential for T7 viability and that our models for the functions encoded by elements are sufficient. To test our initial design, we replaced the left 11,515 base pairs (bp) of the 39,937 bp wild-type genome with 12,179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention.
| S-EPMC1681472 | biostudies-literature
Project description:Pathway refactoring serves as an invaluable synthetic biology tool for natural product discovery, characterization, and engineering. However, the complicated and laborious molecular biology techniques largely hinder its application in natural product research, especially in a high-throughput manner. Here we report a plug-and-play pathway refactoring workflow for high-throughput, flexible pathway construction, and expression in both Escherichia coli and Saccharomyces cerevisiae. Biosynthetic genes were firstly cloned into pre-assembled helper plasmids with promoters and terminators, resulting in a series of expression cassettes. These expression cassettes were further assembled using Golden Gate reaction to generate fully refactored pathways. The inclusion of spacer plasmids in this system would not only increase the flexibility for refactoring pathways with different number of genes, but also facilitate gene deletion and replacement. As proof of concept, a total of 96 pathways for combinatorial carotenoid biosynthesis were built successfully. This workflow should be generally applicable to different classes of natural products produced by various organisms. Biotechnol. Bioeng. 2017;114: 1847-1854. © 2017 Wiley Periodicals, Inc.
| S-EPMC5500230 | biostudies-literature
Project description:There is a lack of free software that provides a professional and smooth experience in text editing and markup for qualitative data analysis. Word processing software like Microsoft Word provides a good editing experience, allowing the researcher to effortlessly add comments to text portions. However, organizing the keywords and categories in the comments can become a more difficult task when the amount of data increases. We present WordCommentsAnalyzer, a software tool that is written in C# using .NET Framework and OpenXml, which helps a qualitative researcher to organize codes when using Microsoft Word as the primary text markup software. WordCommentsAnalyzer provides an effective user interface to count codes, to organize codes in a code hierarchy, and to see various data extracts belonging to each code. It also offers basic visualization tools. We illustrate how to use this software by conducting a preliminary content analysis on Tweets with the #successfulaging hashtag. We also demonstrate that the software has satisfactory performance on a large dataset of Iranian journals abstracts. We hope this open-source software will facilitate qualitative data analysis by researchers who are interested in using Word for this purpose.
| S-EPMC6137411 | biostudies-literature
Project description:The DNA data bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) maintains a primary nucleotide sequence database and provides analytical resources for biological information to researchers. This database content is exchanged with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Resources provided by the DDBJ include traditional nucleotide sequence data released in the form of 27 316 452 entries or 16 876 791 557 base pairs (as of June 2012), and raw reads of new generation sequencers in the sequence read archive (SRA). A Japanese researcher published his own genome sequence via DDBJ-SRA on 31 July 2012. To cope with the ongoing genomic data deluge, in March 2012, our computer previous system was totally replaced by a commodity cluster-based system that boasts 122.5 TFlops of CPU capacity and 5 PB of storage space. During this upgrade, it was considered crucial to replace and refactor substantial portions of the DDBJ software systems as well. As a result of the replacement process, which took more than 2 years to perform, we have achieved significant improvements in system performance.
| S-EPMC3531146 | biostudies-literature
Project description:Background: Evaluation of the quality of research software is a challenging and relevant issue, still not sufficiently addressed by the scientific community. Methods: Our contribution begins by defining, precisely but widely enough, the notions of research software and of its authors followed by a study of the evaluation issues, as the basis for the proposition of a sound assessment protocol: the CDUR procedure. Results: CDUR comprises four steps introduced as follows: Citation, to deal with correct RS identification, Dissemination, to measure good dissemination practices, Use, devoted to the evaluation of usability aspects, and Research, to assess the impact of the scientific work. Conclusions: Some conclusions and recommendations are finally included. The evaluation of research is the keystone to boost the evolution of the Open Science policies and practices. It is as well our belief that research software evaluation is a fundamental step to induce better research software practices and, thus, a step towards more efficient science.
| S-EPMC6883399 | biostudies-literature
Project description:Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer's computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.
| S-EPMC5390961 | biostudies-literature
Project description:BackgroundResearch in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level.ResultsWe introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT) to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology.ConclusionThe Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability), to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.
| S-EPMC2446383 | biostudies-literature
Project description:Maintaining data quality and integrity is important for research studies involving prospective data collection. Data must be entered, erroneous or missing data must be identified and corrected if possible, and an audit trail created.Using as an example a large prospective study, the Missouri Lower Respiratory Infection (LRI) Project, we present an approach to data management predominantly using SAS software. The Missouri LRI Project was a prospective cohort study of nursing home residents who developed an LRI. Subjects were enrolled, data collected, and follow-ups occurred for over three years. Data were collected on twenty different forms. Forms were inspected visually and sent off-site for data entry. SAS software was used to read the entered data files, check for potential errors, apply corrections to data sets, and combine batches into analytic data sets. The data management procedures are described.Study data collection resulted in over 20,000 completed forms. Data management was successful, resulting in clean, internally consistent data sets for analysis. The amount of time required for data management was substantially underestimated.Data management for prospective studies should be planned well in advance of data collection. An ongoing process with data entered and checked as they become available allows timely recovery of errors and missing data.
| S-EPMC2546431 | biostudies-literature
Project description:BackgroundModern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories.ResultsVirtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs.ConclusionSoftware virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.
| S-EPMC2820496 | biostudies-literature