tool development
Recently Published Documents


TOTAL DOCUMENTS

603
(FIVE YEARS 153)

H-INDEX

26
(FIVE YEARS 6)

2022 ◽  
Author(s):  
Amit M Fenn ◽  
Olga Tsoy ◽  
Tim Faro ◽  
Fanny Roessler ◽  
Alexander Dietrich ◽  
...  

Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data. Previous benchmarks focused on isoform quantification and mapping. They neglected event detection tools, which arguably provide the most detailed insights into the alternative splicing process. DICAST offers a modular and extensible framework for the analysis of alternative splicing integrating 11 splice-aware mapping and eight event detection tools. We benchmark all tools extensively on simulated as well as whole blood RNA-seq data. STAR and HISAT2 demonstrated the best balance between performance and run time. The performance of event detection tools varies widely with no tool outperforming all others. DICAST allows researchers to employ a consensus approach to consider the most successful tools jointly for robust event detection. Furthermore, we propose the first reporting standard to unify existing formats and to guide future tool development.


Author(s):  
Jimmy Moore ◽  
Pascal Goffin ◽  
Jason Wiese ◽  
Miriah Meyer

Whether investigating research questions or designing systems, many researchers and designers need to engage users with their personal data. However, it is difficult to successfully design user-facing tools for interacting with personal data without first understanding what users want to do with their data. Techniques for raw data exploration, sketching, or physicalization can avoid the perils of tool development, but prevent direct analytical access to users' rich personal data. We present a new method that directly tackles this challenge: the data engagement interview. This interview method incorporates an analyst to provide real-time personal data analysis, granting interview participants the opportunity to directly engage with their data, and interviewers to observe and ask questions throughout this engagement. We describe the method's development through a case study with asthmatic participants, share insights and guidance from our experience, and report a broad set of insights from these interviews.


2021 ◽  
Author(s):  
Matthew Hartley ◽  
Gerard Kleywegt ◽  
Ardan Patwardhan ◽  
Ugis Sarkans ◽  
Jason R Swedlow ◽  
...  

Despite the importance of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. It accepts bioimaging data associated with publication in any format, from any imaging modality at any scale, as well as reference datasets. The BioImage Archive will improve reproducibility of published studies that derive results from image data. In addition, providing reference datasets to the scientific community reduces duplication of effort and allows downstream analysis to focus on a consistent set of data. The BioImage Archive will also help to generate new insights through reuse of existing data to answer new biological questions, or provision of training, testing and benchmarking data for image analysis tool development. The Archive is available at https://www.ebi.ac.uk/bioimage-archive/.


Author(s):  
Soonkyu Hwang ◽  
Yongjae Lee ◽  
Ji Hun Kim ◽  
Gahyeon Kim ◽  
Hyeseong Kim ◽  
...  

Heterologous production of recombinant proteins is gaining increasing interest in biotechnology with respect to productivity, scalability, and wide applicability. The members of genus Streptomyces have been proposed as remarkable hosts for heterologous production due to their versatile nature of expressing various secondary metabolite biosynthetic gene clusters and secretory enzymes. However, there are several issues that limit their use, including low yield, difficulty in genetic manipulation, and their complex cellular features. In this review, we summarize rational engineering approaches to optimizing the heterologous production of secondary metabolites and recombinant proteins in Streptomyces species in terms of genetic tool development and chassis construction. Further perspectives on the development of optimal Streptomyces chassis by the design-build-test-learn cycle in systems are suggested, which may increase the availability of secondary metabolites and recombinant proteins.


Author(s):  
Tongxiao Cui ◽  
Yi Man ◽  
Feifei Wang ◽  
Shuyang Bi ◽  
Liang Lin ◽  
...  

2021 ◽  
pp. 433-443
Author(s):  
Sonal Shekhawat ◽  
Arshad Iqbal ◽  
Usha Srinivsan ◽  
Pratibha Menon

2021 ◽  
Vol 11 (23) ◽  
pp. 11532
Author(s):  
Tomasz Rak ◽  
Dariusz Rzonca

Simulation models are elements of science that use software tools to solve complex mathematical problems. They are beneficial in areas such as performance engineering and communications systems. Nevertheless, to achieve more accurate results, researchers should use more detailed models. Having an analysis of the system operations in the early modeling phases could help one make better decisions relating to the solution. In this paper, we introduce the use of the QPME tool, based on queueing Petri nets, to model the system stream generator. This formalism was not considered during the first tool development. As a result of the analysis, an alternative design model is proposed. By comparing the behavior of the proposed generator against the one already developed, a better adjustment of the stream to the customer’s needs was obtained. The study results show that appropriately adjusting queueing Petri net models can help produce better streams of data (tokens).


2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 270-270
Author(s):  
Elizabeth Cox ◽  
Thuy Dan Tran ◽  
Hannah Tepsa ◽  
Tonya Roberts

Abstract Self-determination is a core value of person-centered care. Research has shown residents and families want to be involved in decisions about care. Care conferences are one existing structure where residents and families can engage in decision-making about care goals. However, there are few tools to support effective engagement. To inform future tool development, this study sought to understand what resident and family stakeholders value about engaging in care conferences. In virtual meetings, 16 stakeholders identified 3 key areas of engagement: being informed about health/well-being, influencing care goals, and advocating for needs. They indicated current approaches do not achieve these engagement goals, which is particularly problematic during COVID when families cannot engage in person. Stakeholders offered ideas for supporting engagement such as provision of data before the conference. The study has implications for individualizing care conferences and encouraging resident and family engagement in decision-making both during and beyond COVID.


2021 ◽  
pp. 19-26
Author(s):  
Yana Chumburidze ◽  
◽  
Tatiana Omelchenko ◽  

Data loss as a result of threats or natural disasters can lead not only to huge financial losses, but also damage the reputation of the company. The most effective way to protect data from loss is backup. The purpose of the study is to select the most appropriate method of data backup and develop a software tool based on it. We discussed the main methods of data backup such as full backup, incremental backup, differential backup, reverse incremental backup and synthetic backup. We identified the following criteria to determine the most appropriate backup method: backup speed, restore speed, backup repository, reliability, network workload, redundancy. We performed a comparative analysis based on the selected criteria to reveal that the most appropriate method of data backup is reverse incremental backup. A functional model, architecture and interface of the software tool have been designed. The main purpose of the software tool is to implement the method of reverse incremental backup to prevent information loss. The conformity of the backup data obtained as a result of performing a reverse backup to the current state of the system is considered to be the achievement of the goal. We conducted a series of experiments that showed that the backup copy corresponds to the current state of the system.


Sign in / Sign up

Export Citation Format

Share Document