Secure genome processing in public cloud and HPC environments

Aligning next generation sequencing data requires significant compute resources. HPC and cloud systems can provide sufficient compute capacity, but do not offer the required data security guarantees. HPC environments are typically designed for many groups of trusted users and often only include minimal security enforcement, while Cloud environments are mostly under the control of untrusted entities and companies. In this work we present a scalable pipeline approach that enables the use of public Cloud and HPC environments, while improving the patients’ privacy. The applied techniques include adding noisy data, cryptography, and a MapReduce program for the parallel processing of data

The dispositionalist deity: how God creates laws and why theists should care

How does God govern the world? For many theists “laws of nature” play a vital role. But what are these laws, metaphysically speaking? I shall argue that laws of nature are not external to the objects they govern, but instead should be thought of as reducible to internal features of properties. Recent work in metaphysics and philosophy of science has revived a dispositionalist conception of nature, according to which nature is not passive, but active and dynamic. Disposition theorists see particulars as being internally powerful rather than being governed by external laws of nature, making external laws in effect ontologically otiose. I will argue that theists should prefer a dispositionalist ontology, since it leads them toward the theory of concurrentism in divine conservation, rather than occasionalism, and revives the distinction between internal and external teleology. God on this view does not govern the world through external laws of nature, but rather through internal aspects of powerful properties

Mass Production

I argue that mass produced artifacts are ontologically distinctive. If we think of the making of an artifact as the imposition of a creative intention on to some matter, usually through intentional manipulation of the matter, then in the case of mass production, one could say that there is not enough mind to go around! Batches of mass produced objects will have a distinctive essence, lying in the creative act by which they are made, but within a batch, the objects will be distinct from each other, but not essentially distinct

Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells

Cellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity. The resulting data-driven model reproduced all features of measured signaling responses and is sufficient to explain their heterogeneity in individual cells. We present evidence that heterogeneity in the levels of the feedback regulator Wip1 sets cell-specific thresholds for p53 activation, providing means to modulate its response through interacting signaling pathways. Our results demonstrate how excitable signaling networks can provide high specificity, sensitivity and robustness while retaining unique possibilities to adjust their function to the physiology of individual cells