Discussing international perspectives on Open Learning in Brazil: educational politics and pedagogical principles

This paper aims to present some of the new tendencies in Open Learning in the context of international online higher education. These tendencies work as a basis for a discussion of the role of e-learning in online higher education in Brazil. The use of open source technologies and the constant search for quality and innovative pedagogies in the teaching and learning process constitute a new trend in international distance education. The main concern nowadays seems to be with ‘quality’ and ‘widening participation’, which result in initiatives such as ‘Open Educational Resources’. In Brazil, the creation of the Brazilian Open University (UAB) would appear to be consistent with these tendencies. The challenge now is to be able to set up a system that attends to national needs while being open to international tendencies. This paper aims to explore some of these issues, and also to present the most recent freeware technologies used for the purpose of enhancing open learning initiatives

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net