Modelling in tomorrrow's technological landscape - Unveiling Underworld2

Poster presented at the XIV International Workshop on Modelling of Mantle and Lithosphere Dynamics, held at Olérons Island, France, August 31st to September 5th, 2015.<div><br></div><div>It introduces, for those in the community that didn't already know, some of the motivation for Underworld2 and some early concrete examples. In particular our de-facto Underworld 101 benchmark - the Rayleigh Taylor instabilities benchmark, and some detailed interplay with particles as shown in a hot plate example.</div

Additional file 2: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S2. Details of motif occurrence comparison between web-based motif discovery software. The highest scoring motifs discovered in DREME, MEME, RSAT peak-motifs, and TrawlerWeb and their corresponding occurrences are illustrated here. For the highest scoring motif, the number of motif occurrences were expressed as a percentage of the total number of input sequences. *MEME-ChIP pre-processes submitted sequences longer than 100 by trimming them evenly from both ends to get the centered 100 bp sequence and discards trimmed sequences containing only Ns from repeat masking. **MEME motif discovery automatically limits the run to a randomly sampled 600 sequences to reduce run time. (XLSX 576 kb

Additional file 1: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S1. Details of the assessment of TrawlerWeb. Detailed table of Fig. 1b showing, for each ChIP experiment, the ability of individual programs to uncover the correct binding site in yeast. For each individual ChIP experiment, the success or failure of 8 different algorithms including TrawlerWeb is shown. The results from the 6 algorithms (Coverage, AlignACE, Kellis, mdscan, MEME, and MEME-c) were extracted from Harbison et al. 2004 [38]. The matching motifs found by TrawlerWeb are identical to that found by Trawler_standalone (detailed previously in Ettwiller et al. 2007 [5]). The results from RSAT were performed by this study, where the matching motifs found by RSAT were described in the last column. (XLSX 190 kb