Related papers: Realized collaboration across borders - Linux and …
In year 2006 Bio-Linux with the work of Tim Booth and team gives its rising and provide an operating system that was and still specialized in providing a bioinformatic specific software environment for the working needs in this corner of…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
Online creative communities have been able to develop large, open source software (OSS) projects like Linux and Firefox throughout the successful collaborations carried out over the Internet. These communities have also expanded to creative…
This work-in-progress research paper explores the effectiveness of tutorials in interdisciplinary learning environments, specifically focusing on bioinformatics. Tutorials are typically designed for a single audience, but our study aims to…
Software ecosystems are collections of projects that are developed and evolve together in the same environment. Existing literature investigates software ecosystems as isolated entities whose boundaries do not overlap and assumes they are…
We have evolved an IT system that is ubiquitous and pervasive and integrated into most aspects of our lives. Many of us are working on 4th and 5th level refinements in efficiency and functionality. But, we stand on the shoulders of those…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base construction and protein structure determination all benefit from human input. In…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
A timeline is presented which shows the stages involved in converting a bioinformatics software application from a set of standalone algorithms through to a simple web based tool then to a web based portal harnessing Grid technologies and…
"Evolution behaves like a tinkerer" (Francois Jacob, Science, 1977). Software systems provide a unique opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to…
Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…
We analyzed Medical Subject Headings (MeSH) from 21.6 million research articles indexed by PubMed to map this vast space of entities and their relations, providing insights into the origins and future of biomedical convergence. Detailed…
The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems.…
According to different opponents and commercial giants in software industries, the open source style software development has enough capacity to complete successfully the large scale projects. But we have seen many flaws and loops in…
Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…
Most bioinformatics pipelines consist of software components that are tightly coupled to the logic of the pipeline itself. This limits reusability of the individual components in the pipeline or introduces maintenance overhead when they…
A growing gap between progress in biological knowledge and improved health outcomes inspired the new discipline of translational medicine, in which the application of new knowledge is an explicit part of a research plan. Abramson and…
The communities who develop and support open source scientific software packages are crucial to the utility and success of such packages. Moreover, these communities form an important part of the human infrastructure that enables scientific…