A summary of AWS pricing for basic computation, storage, and data transfer.

<p>Prices are current as of 7/05/11.</p>1<p>CPUs are in terms of a 1-GHz Opteron 2007 processor, unless otherwise noted. For example, a machine with four 1-GHz processors would be listed as 4×1.</p>1a<p>CPU is a quad-core Xeon X5570, i.e., two quad-core CPUs, where each core is 4.19 GHz.</p>1b<p>CPU is a quad-core Xeon X5570, and instance includes two NVIDIA Tesla "Fermi" M2050 GPUs.</p>2<p>Costs reflect standard EC2 use with Linux OS. Costs increase when using Windows and decrease when using Reserved Instances (up-front payment) or Spot Instances (user-specified price on unused EC2 capacity).</p>3<p>Within same AWS availability region (e.g., AWS US-East).</p>4<p>Request costs are more difficult to estimate, and are usually more pertinent when databases and other similar services are involved. Programs like IOSTAT can be used to estimate EBS requests.</p

Step-wise framework for creating a scalable NGS computing application.

<p>Using your local computer, ssh into an instance running in AWS. The costs are representative of actual development time, data transfer into and out of the cloud, and the compute time using AWS (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002147#pcbi-1002147-t001" target="_blank">Table 1</a>). The costs presented may vary, as AWS frequently updates their pricing structure. (A) An additional 3 hours were included for installing programs and testing the instance for the prototyping phase. (B) An additional 2 hours were included in developing the scalable application to learn how to use the cluster management software. (C) For the final scaled application, we used a 38-instance cluster.</p

Expression of exon 4 of vasa in zebrafish treated with 100 ppb TCDD within 42 d. Immature female fish were found at 7, 14, and 42 d.

<p>And no fish in 100 ppb group were identified as female by physical observation at 42 d.</p

Cluster analysis (K-means) of the dysregulated genes with their representative Gene Ontology (GO) functional annotations from female (A) and male (B) zebrafish treated with dietary TCDD at 28 d (FDR ≤0.005).

<p>Data are mean fold changes for each treatment group. GO terms are referred to top five terms of Biological Process (BP) category.</p

Two <i>vasa</i> splicing variants in zebrafish (Krøvel <i>et al.</i>, 2004).

<p>Male zebrafish have short vasa mRNA and female zebrafish have both short and long vasa mRNA. A pair of primers was designed crossing exon 2 and exon 6 (arrow). The sequences of primers are: vasa_long_forward 5′-CCCAATATGGATGACTGGGAG-3′; vasa_long_reverse 5′-CAGCACCTCCTGTATAAAAGC-3′. A PCR method was applied to distinguish male and female based on the numbers of bands of PCR products on the gel. Female fish have two bands and male fish have one band. In addition, expression of exon 4 within vasa gene was quantified by real-time QPCR. The sequences are: exon4_forward: 5′-CTTCACGCGTGTCCACCTG-3′; exon4_reverse: 5′-GCTCTTGAATCCTCCATCAGAACC-3′.</p

Expression of exon 4 of vasa in female and male zebrafish treated with TCDD at 28 d.

<p>The asterisk (*) means significant differences in exon 4 expression in 100 ppb group compared to control group with one-way ANOVA.</p

Venn diagram of dysregulated genes in female, immature female and male zebrafish treated with 100 ppb TCDD at 7 d (A), 14 d (B) and 42 d (C).

<p>Venn diagram of dysregulated genes in female, immature female and male zebrafish treated with 100 ppb TCDD at 7 d (A), 14 d (B) and 42 d (C).</p

Representative significant Canonical Pathways and Tox Lists from dysregulated genes in zebrafish treated with TCDD at 28 d.

<p>Representative significant Canonical Pathways and Tox Lists from dysregulated genes in zebrafish treated with TCDD at 28 d.</p

TCDD caused cystic degeneration in nasal epithelium in zebrafish after 42 d of dietary exposure.

<p>A) Well differentiated, orderly, uniform lamella (arrow) of zebrafish in 0 ppb group; B) cystic degeneration of nasal epithelium (arrows) was found in 100 ppb TCDD-treated zebrafish at 42 d (40X).</p

Expression of exon 4 of vasa in zebrafish treated with 100 ppb TCDD within 42 d. Immature female fish were found at 7, 14, and 42 d.

<p>And no fish in 100 ppb group were identified as female by physical observation at 42 d.</p