The robustness, link-species relationship and network properties of model food webs

New results are collected using the Webworld model which simulates evolutionary food web construction with population dynamics (Drossel et al., 2001 [1]). We show that it supports a link-species relationship of neither constant link-density nor constant connectance, and new properties for the food webs are calculated including clustering coefficients and stability in the sense of community robustness to species deletion. Time-series for more than 40 properties of the taxonomic and trophic webs are determined over the course of individual simulations. Robustness is found to be positively correlated with connectance, but negatively with diversity, and we study the long-term development of model webs including the distribution of extinction events in a simulation with 108 speciation event

Investigation into the annotation of protocol sequencing steps in the sequence read archive

BACKGROUND: The workflow for the production of high-throughput sequencing data from nucleic acid samples is complex. There are a series of protocol steps to be followed in the preparation of samples for next-generation sequencing. The quantification of bias in a number of protocol steps, namely DNA fractionation, blunting, phosphorylation, adapter ligation and library enrichment, remains to be determined. RESULTS: We examined the experimental metadata of the public repository Sequence Read Archive (SRA) in order to ascertain the level of annotation of important sequencing steps in submissions to the database. Using SQL relational database queries (using the SRAdb SQLite database generated by the Bioconductor consortium) to search for keywords commonly occurring in key preparatory protocol steps partitioned over studies, we found that 7.10%, 5.84% and 7.57% of all records (fragmentation, ligation and enrichment, respectively), had at least one keyword corresponding to one of the three protocol steps. Only 4.06% of all records, partitioned over studies, had keywords for all three steps in the protocol (5.58% of all SRA records). CONCLUSIONS: The current level of annotation in the SRA inhibits systematic studies of bias due to these protocol steps. Downstream from this, meta-analyses and comparative studies based on these data will have a source of bias that cannot be quantified at present