HepData reloaded: reinventing the HEP data archive

We describe the status of the HepData database system, following a major re-development in time for the advent of LHC data. The new HepData system benefits from use of modern database and programming language technologies, as well as a variety of high-quality tools for interfacing the data sources and their presentation, primarily via the Web. The new back-end provides much more flexible and semantic data representations than before, on which new external applications can be built to respond to the data demands of the LHC experimental era. The HepData re-development was largely motivated by a desire to have a single source of reference data for Monte Carlo validation and tuning tools, whose status and connection to HepData we also briefly review.Comment: 7 pages, 3 figures, Presented at 13th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2010), February 22-27, 2010, Jaipur, Indi

OSHI - Open Source Hybrid IP/SDN networking (and its emulation on Mininet and on distributed SDN testbeds)

The introduction of SDN in IP backbones requires the coexistence of regular IP forwarding and SDN based forwarding. The former is typically applied to best effort Internet traffic, the latter can be used for different types of advanced services (VPNs, Virtual Leased Lines, Traffic Engineering...). In this paper we first introduce the architecture and the services of an "hybrid" IP/SDN networking scenario. Then we describe the design and implementation of an Open Source Hybrid IP/SDN (OSHI) node. It combines Quagga for OSPF routing and Open vSwitch for OpenFlow based switching on Linux. The availability of tools for experimental validation and performance evaluation of SDN solutions is fundamental for the evolution of SDN. We provide a set of open source tools that allow to facilitate the design of hybrid IP/SDN experimental networks, their deployment on Mininet or on distributed SDN research testbeds and their test. Finally, using the provided tools, we evaluate key performance aspects of the proposed solutions. The OSHI development and test environment is available in a VirtualBox VM image that can be downloaded.Comment: Final version (Last updated August, 2014

Evolving NoSQL Databases Without Downtime

NoSQL databases like Redis, Cassandra, and MongoDB are increasingly popular because they are flexible, lightweight, and easy to work with. Applications that use these databases will evolve over time, sometimes necessitating (or preferring) a change to the format or organization of the data. The problem we address in this paper is: How can we support the evolution of high-availability applications and their NoSQL data online, without excessive delays or interruptions, even in the presence of backward-incompatible data format changes? We present KVolve, an extension to the popular Redis NoSQL database, as a solution to this problem. KVolve permits a developer to submit an upgrade specification that defines how to transform existing data to the newest version. This transformation is applied lazily as applications interact with the database, thus avoiding long pause times. We demonstrate that KVolve is expressive enough to support substantial practical updates, including format changes to RedisFS, a Redis-backed file system, while imposing essentially no overhead in general use and minimal pause times during updates.Comment: Update to writing/structur

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

<p>Abstract</p> <p>Background</p> <p>In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user.</p> <p>Results</p> <p>We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects.</p> <p>Conclusion</p> <p>Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.</p

C to O-O Translation: Beyond the Easy Stuff

Can we reuse some of the huge code-base developed in C to take advantage of modern programming language features such as type safety, object-orientation, and contracts? This paper presents a source-to-source translation of C code into Eiffel, a modern object-oriented programming language, and the supporting tool C2Eif. The translation is completely automatic and supports the entire C language (ANSI, as well as many GNU C Compiler extensions, through CIL) as used in practice, including its usage of native system libraries and inlined assembly code. Our experiments show that C2Eif can handle C applications and libraries of significant size (such as vim and libgsl), as well as challenging benchmarks such as the GCC torture tests. The produced Eiffel code is functionally equivalent to the original C code, and takes advantage of some of Eiffel's object-oriented features to produce safe and easy-to-debug translations

3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

CRAID: Online RAID upgrades using dynamic hot data reorganization

Current algorithms used to upgrade RAID arrays typically require large amounts of data to be migrated, even those that move only the minimum amount of data required to keep a balanced data load. This paper presents CRAID, a self-optimizing RAID array that performs an online block reorganization of frequently used, long-term accessed data in order to reduce this migration even further. To achieve this objective, CRAID tracks frequently used, long-term data blocks and copies them to a dedicated partition spread across all the disks in the array. When new disks are added, CRAID only needs to extend this process to the new devices to redistribute this partition, thus greatly reducing the overhead of the upgrade process. In addition, the reorganized access patterns within this partition improve the array’s performance, amortizing the copy overhead and allowing CRAID to offer a performance competitive with traditional RAIDs. We describe CRAID’s motivation and design and we evaluate it by replaying seven real-world workloads including a file server, a web server and a user share. Our experiments show that CRAID can successfully detect hot data variations and begin using new disks as soon as they are added to the array. Also, the usage of a dedicated partition improves the sequentiality of relevant data access, which amortizes the cost of reorganizations. Finally, we prove that a full-HDD CRAID array with a small distributed partition (<1.28% per disk) can compete in performance with an ideally restriped RAID-5 and a hybrid RAID-5 with a small SSD cache.Peer ReviewedPostprint (published version