Example based learning in programming language is a common approach when mastering the art of programming. It encourages students to reuse the code of previously analyzed examples in solving a new problem [1][2]. Gomez-Albarran [3] in a synthesis report about teaching and learning of programming stressed that example-based learning is a natural way of learning. To support online learning from e...

Three principal approaches have been proposed for inferring the set of transcripts expressed in RNA samples using RNA-seq. The simplest approach uses curated annotations, which assumes the transcripts in a sample are a subset of the transcripts listed in a curated database. A more ambitious method involves aligning reads to a reference genome and using the alignments to infer the transcript str...

Motivation: Alternative splicing has recently emerged as a key mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms. Although several online resources devoted to alternative splicing analysis are available they may suffer from limitations related both to the computational methodologies adopted and to the extent of the annotations they pro...

MOTIVATION Alternative splicing has recently emerged as a key mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms. Although several online resources devoted to alternative splicing analysis are available they may suffer from limitations related both to the computational methodologies adopted and to the extent of the annotations they prov...

Increasing numbers of museums and cultural institutions are using 3D scanning techniques to preserve cultural artefacts as 3D digital models and to provide curators, scholars and the general public with a richer experience when accessing online exhibitions. However there are a number of challenges associated with the development, maintenance and curation of 3D digital collections. In particular...

PANTHER (Protein Analysis THrough Evolutionary Relationships, http://pantherdb.org) is a widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. Recent development has been focused in three main areas: genome coverage, functional information ('annotation') coverage and accuracy, and improved g...

SUMMARY MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interacti...

The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been up...

Motivation The Sequence Read Archive (SRA) contains raw data from many different types of sequence projects. As of 2017, the SRA contained approximately ten petabases of DNA sequence (10 16 bp). Annotations of the data are provided by the submitter, and mining the data in the SRA is complicated by both the amount of data and the detail within those annotations. Here, we introduce PARTIE, a part...

It is a common opinion that today’s digital libraries (DL) can no longer be simple “expositions’ of digital objects. Users should no more be passive readers, they need to interact with the library, add their annotations and tags, personalize their experience and collaborate with each other. Web 2.0 technologies, such as social bookmarking and online discussions, are already being applied in DLs...