Abstract

Abstract

Abstract
Background: Gene expression studies are an important tool in biological and biomedical research. The signal carried in expression profiles helps derive signatures for the prediction, diagnosis and prognosis of different diseases. Data science and specifically machine learning have many applications in gene expression analysis. However, as the dimensionality of genomics datasets grows, scalable solutions become necessary. Methods: In this paper we review the main steps and bottlenecks in machine learning pipelines, as well as the main concepts behind scalable data science including those of concurrent and parallel programming. We discuss the benefits of the Dask framework and how it can be integrated with the Python scientific environment to perform data analysis in computational biology and bioinformatics. Results: This review illustrates the role of Dask for boosting data science applications in different case studies. Detailed documentation and code on these procedures is made available at https:// github. com/martaccmoreno/gexp-ml-dask. Conclusion: By showing when and how Dask can be used in transcriptomics analysis, this review will serve as an entry point to help genomic data scientists develop more scalable data analysis procedures.

Abstract
Modern containerized distributed systems, such as big data storage and processing stacks or micro-service based applications, are inherently hard to monitor and optimize, as resource usage does not directly match hardware resources due to multiple virtualization layers. For instance, inter-application traffic is an important factor in as it directly indicates how components interact, it has not been possible to accurately monitor it in an application independent way and without severe overhead, thus putting it out of reach of cloud platforms. In this paper we present an efficient black-box monitoring approach for gathering detailed structural information of collaborating processes in a distributed system that can be queried for various purposes, as it includes both information about processes, containers, and hosts, as well as resource usage and amount of data exchanged. The key to achieving high detail and low overhead without custom application instrumentation is to use a kernel-aided event driven strategy. We validate a prototype implementation by applying it to multi-platform microservice deployments, evaluate its performance with micro-benchmarks, and demonstrate its usefulness for container placement in a distributed data storage and processing stack (i.e., Cassandra and Spark).

Abstract
Logs are still the primary resource for debugging distributed systems executions. Complexity and heterogeneity of modern distributed systems, however, make log analysis extremely challenging. First, due to the sheer amount of messages, in which the execution paths of distinct system components appear interleaved. Second, due to unsynchronized physical clocks, simply ordering the log messages by timestamp does not suffice to obtain a causal trace of the execution. To address these issues, we present Horus, a system that enables the refinement of distributed system logs in a causally-consistent and scalable fashion. Horus leverages kernel-level probing to capture events for tracking causality between application-level logs from multiple sources. The events are then encoded as a directed acyclic graph and stored in a graph database, thus allowing the use of rich query languages to reason about runtime behavior. Our case study with TrainTicket, a ticket booking application with 40+ microservices, shows that Horus surpasses current widely-adopted log analysis systems in pinpointing the root cause of anomalies in distributed executions. Also, we show that Horus builds a causally-consistent log of a distributed execution with much higher performance (up to 3 orders of magnitude) and scalability than prior state-of-the-art solutions. Finally, we show that Horus' approach to query causality is up to 30 times faster than graph database built-in traversal algorithms.