Governance: a challenge for international collaborative research and development: Some recent experiences from Brazil.

Abstract - International partnership to carry out collaborative research and development programs has been implemented for a long time. However, with globalization, the economic, social, political and cultural diversity of interacting partners reached levels where this variety of collaborators often has shown some weaknesses in issues like governance. Strong and sound partnerships must be manageable in order to ensure the achievement of the set objectives. Embrapa, as a Brazilian public agricultural research and development institution that coordinates the Brazilian National Agricultural Research System (NARS), has acquired some experience in strengthening the inter-institutional relationship across continents. Recently, Embrapa was involved in a new research program focusing participatory and adaptive research to improve the production and marketability of small ruminants in arid areas of Latin America. The program is supported by the International Fund for Agricultural Development (IFAD) and coordinated by a CGIAR-Center - the International Center for Agricultural Research in the Dry Areas (ICARDA). The program was started at the end of 2003 with the participation of two countries, Brazil and Mexico. Brazil is being represented by Embrapa and Mexico by the National Research Institute for Forestry, Agriculture and Livestock (INIFAP). The program has a Steering Committee, where all involved institutions have a representative member, including the donor (IFAD) and research institutions (CGIAR/ICARDA, Embrapa for Brazil and INIFAP for Mexico). The so far obtained results show the viability of international collaborative research programs to improve fund raising and to optimize the use of available human resources.Proceedings 4th Internation Symposium-cum-Workshop Red Cientifica Alemania Lationamericana (RECALL) on International Scientific Cooperation in Higher Education: Participation, Partnership and Perspectives healt in Talca, Chile, Nov. 28 to Dec., 4, 2005

Open Access SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16 % to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption

Erratum to "SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler" [GigaScience, (2012), 1, 18]

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Data from: Phylogenomics resolves the timing and pattern of insect evolution

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives.

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives. This file includes 14 supplementary archives which are in detail described in the README