NGS y Metagenómica

The Next Generation Sequencing (NGS) allows to sequence the whole genome of an organism, compared to Maxam and Gilbert and Sanger sequencing that only allow to sequence, hardly, a single gene. Removing the separation of DNA fragments by electrophoresis, and the development of techniques that let the parallelization (analysing simultaneously several DNA fragments) have been crucial for the improvements of this process. The new companies in this ambit, Roche and Illumina, bet for different protocols to achieve these goals. Illumina bets for the sequencing by synthesis (SBS), requiring the library preparation and the use of adapters. Likewise, Illumina has replaced Roche because its lower rate of misincorporation, making it ideal for studies of genetic variability, transcriptomic, epigenomic, and metagenomic, in which this study will focus. However, it is noteworthy that the last progress in sequencing is carried out by the third generation sequencing, using nanotechnology to design small sequencers that sequence the whole genome of an organism quickly and inexpensively. Moreover, they provide more reliable data than current systems because they sequence a single molecule, solving the problem of synchronisation. In this way, PacBio and Nanopore allow a great progress in diagnostic and personalized medicine. Metagenomics provide to make a qualitative and quantitative analysis of the various species present in a sample. The main advantage of this technique is the no necessary isolation and growth of the species, allowing the analysis of nonculturable species. The Illumina protocol studies the variable regions of the 16S rRNA gene, which contains variable and not variables regions providing a phylogenetic classification. Therefore, metagenomics is a topic of interest to know the biodiversity of complex ecosystems and to study the microbiome of patients given the high involvement with certain microbial profiles on the condition of certain metabolic diseases.

Insights into the Fallback Path of Best-Effort Hardware Transactional Memory Systems

Current industry proposals for Hardware Transactional Memory (HTM) focus on best-effort solutions (BE-HTM) where hardware limits are imposed on transactions. These designs may show a significant performance degradation due to high contention scenarios and different hardware and operating system limitations that abort transactions, e.g. cache overflows, hardware and software exceptions, etc. To deal with these events and to ensure forward progress, BE-HTM systems usually provide a software fallback path to execute a lock-based version of the code. In this paper, we propose a hardware implementation of an irrevocability mechanism as an alternative to the software fallback path to gain insight into the hardware improvements that could enhance the execution of such a fallback. Our mechanism anticipates the abort that causes the transaction serialization, and stalls other transactions in the system so that transactional work loss is mini- mized. In addition, we evaluate the main software fallback path approaches and propose the use of ticket locks that hold precise information of the number of transactions waiting to enter the fallback. Thus, the separation of transactional and fallback execution can be achieved in a precise manner. The evaluation is carried out using the Simics/GEMS simulator and the complete range of STAMP transactional suite benchmarks. We obtain significant performance benefits of around twice the speedup and an abort reduction of 50% over the software fallback path for a number of benchmarks.