15 downloads
94 views

MerCat (“ Mer - Cat enate”) is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. Using assembled contigs and raw sequence reads from any platform as input, MerCat performs k-mer...

["Bioinformatics","Computational Biology","Data Science","Scientific Computing and Simulation","Software Engineering"]
doi:10.7287/peerj.preprints.2825v1
25 views

Introduction Computational reproducibility refers to the possibility of reconstructing all the steps of a workflow that connects raw data, processed data and results: it is a fundamental issue in the omic studies because of the complex and high-dimensional nature...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.2823v1
1 download
9 views

The HUBzero platform is an infrastructure enabling online scientific communities to collaborate and share information and computational resources as they explore scientific phenomena. HUBzero has been adopted by the Regenstrief Center for Healthcare Engineering...

["Data Science","Visual Analytics"]
doi:10.7287/peerj.preprints.2819v1
60 downloads
484 views

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates; however, filtering criteria remain challenging, and systems biology approaches...

["Bioinformatics","Computational Biology","Data Science","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.106
10 downloads
165 views

Motivated by the increasing amount of voices who ask for careful consideration of what context-rich data analysis methods can tell us about the activities of human collectives, we contribute an argumentation that employs a dialectic of literature on the philosophy...

["Data Mining and Machine Learning","Data Science","Network Science and Online Social Networks","Social Computing","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2789v1
5 downloads
47 views

This document describes a novel way to extract structure information from plain text using Markov Decision Process. In the age of big data, unstructured information such as text, photos and videos be- comes abundant. However, data warehouse requires structured...

["Data Science"]
doi:10.7287/peerj.preprints.2774v1
48 downloads
313 views

While most challenges organized so far in the Semantic Web domain are focused on comparing tools with respect to different criteria such as their features and competencies, or exploiting semantically enriched data, the Semantic Web Evaluation Challenges series,...

["Data Science","Digital Libraries","Emerging Technologies","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.105
53 downloads
196 views

Debugging software is an inevitable chore, often difficult and more time-consuming than expected, giving it the nickname the “ dirty little secret of computer science.” Surprisingly, we have little knowledge on how software engineers debug software problems in...

["Computer Education","Data Science","Software Engineering"]
doi:10.7287/peerj.preprints.2743v1
143 downloads
970 views

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare,...

["Bioinformatics","Data Science","Databases","Emerging Technologies","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2522v2
88 downloads
460 views

Shotgun metagenomics of microbial communities reveals information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial, but very challenging step, due to the complexity of the underlying biological...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.2626v3
55 downloads
574 views

Software is data, but it is not just data. While "data" in computing and information science can refer to anything that can be processed by a computer, software is a special kind of data that can be a creative, executable tool that operates on data. However, software...

["Data Science","Scientific Computing and Simulation","Software Engineering"]
doi:10.7287/peerj.preprints.2630v1
181 downloads
420 views

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates, however filtering criteria remain challenging, and systems biology approaches...

["Bioinformatics","Computational Biology","Data Science","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2007v2
32 downloads
79 views

While most challenges organized so far in the Semantic Web domain are focused on comparing tools with respect to different criteria such as their features and competencies, or exploiting semantically enriched data, the Semantic Web Evaluation Challenges series,...

["Data Science","Digital Libraries","Emerging Technologies","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2616v1
116 downloads
333 views

The ability to recognise new research trends early is strategic for many stakeholders, such as academics, institutional funding bodies, academic publishers and companies. While the state of the art presents several works on the identification of novel research...

["Artificial Intelligence","Data Science","Digital Libraries"]
doi:10.7287/peerj.preprints.2306v3
27 downloads
104 views

Jupyter Notebooks empower scientists to create executable documents that include text, equations, code and figures. Notebooks are a simple way to create reproducible and shareable workflows. The Jupyter developers have also released a multi-user notebook environment:...

["Data Science","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.2577v2

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