BitTorious: global controlled genomics data publication,research and archiving via BitTorrent extensions

Background

Centralized silos of genomic data are architecturally easier to initially design, develop and deploy than distributed models. However, as interoperability pains in EHR/EMR, HIE and other collaboration-centric life sciences domains have taught us, the core challenge of networking genomics systems is not in the construction of individual silos, but the interoperability of those deployments in a manner embracing the heterogeneous needs, terms and infrastructure of collaborating parties. This article demonstrates the adaptation of BitTorrent to private collaboration networks in an authenticated, authorized and encrypted manner while retaining the same characteristics of standard BitTorrent.

Results

The BitTorious portal was sucessfully used to manage many concurrent domestic Bittorrent clients across the United States: exchanging genomics data payloads in excess of 500GiB using the uTorrent client software on Linux, OSX and Windows platforms. Individual nodes were sporadically interrupted to verify the resilience of the system to outages of a single client node as well as recovery of nodes resuming operation on intermittent Internet connections.

Conclusions

The authorization-based extension of Bittorrent and accompanying BitTorious reference tracker and user management web portal provide a free, standards-based, general purpose and extensible data distribution system for large ‘omics collaborations.     

基于网络微平台教学的微生物学实验精细化及个性化教学改革

为更好地适应信息化时代的微生物学实验教学特点,全面落实培养学生创新能力的全新微生物学实验教学手段体系的目标,在本次教改过程中,我们根据学生性格特点、学习成绩、爱好取向等多方面因素,对实验课程进行了精细化、个性化的分组,同时针对性地选取现代化网络微平台开展实验教学(课堂派、微助教、雨课堂、UMU、班级优化大师等),并进行了为期一年的试点改革。改革结果发现,基于网络微平台的精细化及个性化的混合交互式教学,促进了教学由"定性分析"向"精准定量分析"转变。学生深感多层次微生物学实验教学体系配合精细化教学手段和工具,能更加有助于个性化实践学习,极大激发了学习兴趣,提高了学习效果,全面提升了学生的综合创新能力。     

I-BIND: International Blue intensity network development working group

Blue Intensity (BI) is coming of age in dendrochronology, although some methodological challenges still need resolution. In the last 20 years, 59 papers have been published focussing mainly on climatological based studies, although BI has also been shown to be useful both for historical dating and dendroecological studies. This short paper briefly reviews the BI method development of the last two decades and introduces a new collaborative initiative called I-BIND (International Blue Intensity Network Development Working Group), which is supported by the Association of Tree-Ring Research. The main aims of I-BIND are to promote continued methodological development, communicate best practice via workshops, encourage the development of BI data networks to enhance both dendroclimatology and dendro-historical dating, and to create a rich environment in which innovative and novel initiatives can be explored and discussed.     

Origins of weedy rice revealed by polymorphisms of chloroplast DNA sequences and nuclear microsatellites

Conspecific weeds that permanently infest worldwide agroecosystems are evolved from their crop species. These weeds cause substantial problems for crop production by competing for resources in agricultural fields. Weedy rice represents such a conspecific weed infesting rice ecosystems, and causing tremendous rice yield losses owing to its strong competitiveness and abundant genetic diversity, likely resulted from its complex origins. Here, we report the use of chloroplast DNA (cpDNA) fingerprints to determine whether weedy rice is evolved from its wild (exo‐feral) or cultivated (endo‐feral) rice progenitor as the maternal donor in recent hybridization events. In addition, we also applied nuclear simple sequence repeat (SSR) markers to confirm the exo‐feral or endo‐feral origins of weedy rice accessions determined by the cpDNA fingerprints. We found that the studied weedy rice accessions evolved either from their wild or cultivated rice progenitor, as the maternal donor, based on the cpDNA network and structure analyses. Combined analyses of cpDNA and nuclear SSR markers indicated that a much greater proportion of weedy rice accessions had the endo‐feral origin. In addition, results from the genetic structure of nuclear SSR markers indicated that weedy rice accessions from the endo‐feral pathway are distinctly associated with either indica or japonica rice cultivars, suggesting their complex origins through crop–weed introgression. The complex pathways of origin and evolution could greatly promote genetic diversity of weedy rice. Therefore, innovative methods should be developed for effective weedy rice control.