Offers an interactive guidance to a systematic and scientifically critical interpretation of optical coherence tomography (OCT) images. The Clinical Atlas of Intravascular OCT consists of eight separate chapters offering the following contents: (i) Principles of OCT, (ii) Artefacts, (iii) Atherosclerosis, (iv) Evaluation of metallic stents, (v) 3D-OCT, (vi) Evaluation of bio-resorbable scaffold,s (vii) Miscellaneous (vein grafts, peripheral vessels, etc.), and (viii) New frontiers in OCT imaging.
Consists of an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn can be used for entering and annotating announcement information. It offers a collection of services and widgets that can be embedded in external websites, and display pre-programmed filtered lists of announcements.
Interactively calculates the Dynamic Programming (DP) matrix in real time. SAT also visually illustrates the consequences of tweaking the various parameters of the algorithm. This simple software tool will not only be useful for teachers and students of bioinformatics courses but also to future bioinformatics developers as an error check tool when they start implementing this algorithm for the first time.
Provides interactive modules to help students and researchers understand key bioinformatics concepts. TeachEnG is an interactive online educational tool for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction. It proposes instructional games which allow students to align sequences by hand, fill out the dynamic programming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony and Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithms. With an easily accessible interface and instant visual feedback, TeachEnG will help promote active learning in bioinformatics.
Provides a web platform for simulations and modelling tools, and other resources like online courses, short courses and full-fledged tool-powered curricula. nanoHUB.org hosts over 3000 content items and more than 260 tools and proposes a list of tools selected for their efficiency and other quality criteria. Each tool is displayed on the platform with some data like numbers of its users, community’s reviews and questions, classroom usage or citations in the literature.
Stores code and certain raw materials for a detailed RNA-seq tutorial. Informatics for RNA-seq is an educational tutorial and working demonstration pipeline for RNA-seq analysis including an introduction to: cloud computing, next generation sequence file formats, reference genomes, gene annotation, expression analysis, differential expression analysis, alternative splicing analysis, data visualization, and interpretation.
Allows students to learn infectious disease concepts by using a modern computational and modeling approach while not requiring students to read or write computer code. DSAIDE permits users to explore different topics in infectious disease epidemiology. The package is structured in a modular way allowing users to directly interact with and modify the underlying simulations.
Provides algorithms related to RNA structure and RNA-RNA interactions prediction. RNA-Playground is available at an online and a locale application. The web interface was developed to (i) assit users to understand and follow the algorithms, (ii) ease the generation of interesting examples for different aspects to teach, and (iii) provide master solutions for comparison with users’ calculations or implementations.
Allows the investigation of visualization methods in intuitive ways based on filtering. BioVis Explorer is a web application informing users about visualization techniques. This method assists users in studying biological data sets proposed in publications from top-tier journals and conferences within a time range from 2000 to 2016. It also proposes taxonomy of various aspects of the data and visualization methods.
Informs about text visualization techniques. Text Visualization Browser is a web application that can be used for getting an overview of the field, teaching purposes, and finding related work based on various categories defined in a survey taxonomy. It classifies about 30 text visualization methods with regard to data source, underlying text representation and processing method, temporal aspects, and supports user interactions.
Presents a list of visualization technique thumbnails organized in a grid. SentimentVis Browser is a web application allowing users to access to category statistics and a summary table with an overview of the complete categorization. It assists users in monitoring of public opinion in social media, literature analysis for digital humanities, or support for research of sentiment and stance in linguistics and natural language processing (NLP). Users can submit additional entries thanks to a form available from the top panel.
Clusters big data and interactive visualizations including 3D views, cluster selection and zoom features. ClusterEnG aims at educating the user about the similarities and differences between various clustering algorithms and provides clustering tutorials that demonstrate potential pitfalls of each algorithm. The user can choose the clustering method used by the tool. It implements seven algorithms include k-means, k-medoids, affinity propagation, spectral clustering, Gaussian mixture model, hierarchical clustering and DBSCAN.
Provides a visualization system for comparing large collections of words. TextDNA is a web-based visualization system that uses a configurable colorfield design combined with tailored interaction techniques to enable multiscale exploration of word usage data. Users can interactively reconfigure how data is mapped to color and position within these colorfields to answer a variety of questions.
Offers the opportunity to perform controlled crosses with model organisms. CGS provides populations of Drosophila, Arabidopsis or mice with unknown patterns of inheritance and gives students the tools to design and perform experiments to discover these patterns. It allows biology students to apply lessons in Mendelian genetics to real-world situations. The tool can be used as a primary laboratory module for introductory biology or genetics courses, or as a supplement to a hands-on genetics module with real organisms.
Provides a virtual laboratory class for undergraduate students of Genetics in Biology. Mutate emulates the so-called fluctuation test whose aim is to distinguish between spontaneous and adaptive mutation hypotheses in bacteria. It permits to train students in some multidisciplinary aspects of current genetics as sequence databases, DNA mutations and hypothesis testing, while introducing the fluctuation test.
Simplifies the recognition of the proteins encoded within a DNA sequence. StarORF transcribes the DNA sequence into RNA. It translates the RNA into all the potential open reading frames (ORFs). This tool offers a solution to recognize the translation frame that results in the longest protein coding sequence.
Mimics mating experiments between organisms that are genetically different across a range of traits. StarGenetics permits researchers to investigate the nature of the traits in question. It is useful for students that want to learn genetic experimental design and genetic concepts. This tool serves for the construction of exercises for genetic experiments and for the simulation of crosses between non-model organisms.
Provides a platform allowing the conduction of research projects by high school students of different ages, either under direct teacher supervision or as homework. [email protected] exploits freely accessible bioinformatics tools and databases to construct its environment. It allows enquiry-based learning in high schools. This tool can guide the students in the bioinformatics-based projects and understand the basics of the bioinformatics methods and resources underlying each activity.
Annotates and explains available next-generation sequencing (NGS) techniques and their data analysis methods. SequencEnG is an web resource that contains about 60 NGS techniques organized into a knowledge tree based on genetic or epigenetic information being assayed. Interactive data analysis pipelines are available for RNA-seq, ChIP-seq, Hi-C, and Whole Genome Bisulfite Sequencing (WGBS), with lists of major bioinformatics tools for each analysis step in the pipelines. It can be useful for students and researchers entering bioinformatics and the NGS field.
A collaborative next-generation sequencing (NGS) resource. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.
Offers a wide range of services and repositories widely used in genomic research as well as documentation and material for training. eBiokit is a portable bioinformatics educational platform reducing dependences on the internet. It provides computing platform and database system containing up to 6 terabytes of biological data and software tools of relevance to bioinformatics researching.
Allows users to explore, analyze, and gain insight into such data. This online database contains several analytical and interactive visual methods allowing users to study multifaceted scientific data. The database purposes are exploration and analysis of single facets of such data. Then it transmits results from data analysis to users. One of its functions is to synthesize different types of information from different sources into a unified representation of the data.
Informs users on the various existing visualization techniques. This online library brings a meaningful overview of graph structures, to highlight central objects, to show similar objects, and to reveal outliers. It includes different filters to assist users in their query: a timeline, a keywords table, or color selectors. For each user request, this database provides a list of results containing publications related to a visualization technique.
Supplies techniques that assists users in development of software. Performance Visualization is an online library that classifies different technique of visualization and categorizes them. This resource is useful to better understand how different software is run on such machines and optimize their performance. It supplies a context-based classification and survey of existing performance visualizations.
Informs users about visualization techniques. SetViz is an online platform providing information and classifying set visualization techniques into six categories. The techniques in each category exhibit similar scalability and readability properties as well as design considerations. This resource proposes software implementations, demos and videos about the surveyed techniques.
Classifies existing visualization techniques. Dynamic Graph Visualization covers the evolution of relationship between effective diagrams, entities in readable and scalable. This online library contains several publication references that are tag and categorize thanks to a hierarchical taxonomy. Each graph is represented as static graphs based on a timeline or animated diagrams.
Supplies a collection of cook-book like manuals constructed for various microarray designs. MAGMA aims to suggest solution for the exploitation of microarrays data. It is subdivided into eight different sections, representing several steps in microarrays investigation process.
Provides animated resources of 75 experiments that contributed to modern genetics. DNA form the beginning is subdivided 41 major topics, classified into three sections: classical genetics, molecules of genetics, genetic organization and control. It offers several links, offering the possibility to investigate other sources of information.
Consists of a platform designed as a repository of courses, applications, serious games and information related to science. Learn.Genetics is dedicated to the vulgarization of science and health for non-expert users.
Offers free, open and online courses in DNA design. Synthetic Biology One addressed first-year master’s students in a life science background. It provides serious games, courses, lessons, units and quizzes around DNA knowledge. Lessons offered on the platform are designed to be as modular as possible and are classified by subject.
Provides a survey of the literature in a format which facilitates easy scanning. ALTBIB includes citations from published articles, books, book chapters, and technical reports. It can be easy searchable through a friendly-user interface. The user can limit the search to a particular field. Users seeking a finer degree of precision in retrieval than available through either ALTBIB's standard Basic Search screen or Limits option searching can use the advanced searching features.
Enables the open sharing of research outputs and educational materials. SPARC aims to democratize access to knowledge, accelerate discovery, and increase the return on investment in research and education. It places a premium on collaboration and collective action, and works to advance this mission through the development and leadership of active coalitions. This platform promotes changes to both infrastructure and culture.
Provides resources in genetics education and discovery including labs, experiments and career information. GeneEd is composed of ten sections: cell biology; DNA, genes, chromosomes; heredity/inheritance patterns; epigenetics/inheritance and the environment; genetic conditions; evolution; biostatistics; biotechnology; DNA forensics; and top issues in genetics.
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