SUMMARY: Spatial and temporal intra-tumor heterogeneity drives tumor evolution and therapy resistance. Existing visualization tools often fail to capture both dimensions simultaneously. To address this, we developed Jellyfish, a tool that integrates phylogenetic and sample trees into a single plot, providing a holistic view of tumor evolution and capturing both spatial and temporal evolution. Available as a JavaScript library and R package, Jellyfish generates interactive visualizations from tumor phylogeny and clonal composition data. We demonstrate its ability to visualize complex subclonal dynamics using data from ovarian high-grade serous carcinoma. AVAILABILITY AND IMPLEMENTATION: Jellyfish is freely available with MIT license at https://github.com/HautaniemiLab/jellyfish (JavaScript library) and https://github.com/HautaniemiLab/jellyfisher (R package).

Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments. We propose ViraPipe, a scalable metagenome analysis pipeline that is able to analyze thousands of human microbiomes in parallel in tolerable time. The pipeline is tuned for analyzing viral metagenomes and the software is applicable for other metagenomic analyses as well. ViraPipe integrates parallel BWA-MEM read aligner, MegaHit De novo assembler, and BLAST and HMMER3 sequence search tools. We show the scalability of ViraPipe by running experiments on mining virus related genomes from NGS datasets in a distributed Spark computing cluster. Results: ViraPipe analyses 768 human samples in 210 minutes on a Spark computing cluster comprising 23 nodes and 1288 cores in total. The speedup of ViraPipe executed on 23 nodes was 11x compared to the sequential analysis pipeline executed on a single node. The whole process includes parallel decompression, read interleaving, BWA-MEM read alignment, filtering and normalizing of non-human reads, De novo contigs assembling, and searching of sequences with BLAST and HMMER3 tools. Contact: [email protected]. Availability and implementation: https://github.com/NGSeq/ViraPipe.

Acquiring knowledge from continuous and heterogeneous data streams is a prerequisite for Internet of Things (IoT) applications. Semantic technologies provide comprehensive tools and applicable methods for representing, integrating, and acquiring knowledge. However, resource-constraints, dynamics, mobility, scalability, and real-time requirements introduce challenges for applying these methods in IoT environments. We study how to utilize semantic IoT data for reasoning of actionable knowledge by applying state-of-the-art semantic technologies. For performing these studies, we have developed a semantic reasoning system operating in a realistic IoT environment. We evaluate the scalability of different reasoning approaches, including a single reasoner, distributed reasoners, mobile reasoners, and a hybrid of them. We evaluate latencies of reasoning introduced by different semantic data formats. We verify the capabilities of promising semantic technologies for IoT applications through comparing the scalability and real-time response of different reasoning approaches with various semantic data formats. Moreover, we evaluate different data aggregation strategies for integrating distributed IoT data for reasoning processes.

Demand for new efficient methods for processing large-scale heterogeneous data in real-time is growing. Currently, one key challenge in Big Data is performing low-latency analysis with real-time data. In vehicle traffic, continuous high speed data streams generate large data volumes. Harnessing new technologies is required to benefit from all the potential this data withholds. This work studies the state-of-the-art in distributed and parallel computing, storage, query and ingestion methods, and evaluates tools for periodical and real-time analysis of heterogeneous data. We also introduce a Big Data cloud platform with ingestion, analysis, storage and data query APIs to provide programmable environment for analytics system development and evaluation.