File format | EPFL Graph Search

A file format is a standard way that information is encoded for storage in a . It specifies how bits are used to encode information in a digital storage medium. File formats may be either proprietary or free. Some file formats are designed for very particular types of data: PNG files, for example, store bitmapped using lossless data compression. Other file formats, however, are designed for storage of several different types of data: the Ogg format can act as a container for different types of multimedia including any combination of audio and video, with or without text (such as subtitles), and metadata. A can contain any stream of characters, including possible control characters, and is encoded in one of various character encoding schemes. Some file formats, such as HTML, scalable vector graphics, and the source code of computer software are text files with defined syntaxes that allow them to be used for specific purposes. Specifications File formats often have a pu

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

Whole Genome Sequencing is a process in the field of bioinformatics that transforms biological samples of DNA into an electronic dataset of genetic bases. The process consists of two sequential components. First, the laboratory process of sequencing transforms the biological DNA samples into a digital format by transcribing the sequence of bases that make up short snippets of DNA. Second, a genomic workflow uses software to transform this data into a representation that is useful for genomic analysis. Recent advancements in High-Throughput Sequencing technology enable the laboratory phase to produce data faster and at a lower cost than prior techniques were capable of. The applications and file formats used in workflows have not undergone commensurate technological advancement in order to accommodate this deluge of genomic data. This thesis introduces a redesign of genomic workflows, their component applications, and the underlying file formats in order to scale out workflows across a data center. The design builds upon on two design components. First, a unified file format supplants the myriad existing formats in order to accommodate scale-out multi-machine I/O. The file format imposes minimal feature requirements upon the storage system, thereby enabling its use in high- performance systems for processing and cost-effective cold storage systems for long-term storage. Second, a new cloud computing framework provides an API for composing workflows in an abstract logical description and delegating the execution of the logic to a common runtime. The framework's runtime executes the logical workflow description on scale-out hardware resources while abstracting the execution details. We combine the file format and framework to build a new set of workflows that scale out across data center resources. These scale-out workflows incorporate existing workflow applications (compartmentalized into libraries that the framework invokes) and new applications that leverage the features provided by the scale-out architecture. All workflows delegate work distribution and task concurrency to the framework's runtime and utilize a common set of subcomponents for auxiliary code (e.g., I/O with various storage systems, processing different file formats). These workflows are able to scale out across a data center to the point of saturating the throughput of one or more hardware resources.

EPFL2019

Real-time animation and motion capture in Web Human Director (WHD)

Daniel Thalmann

Motion capture systems usually work in conjunction with complex 3D applications, such as 3D Studio Max by Kinetix or Maya by Alias/Wavefront. Once models have been created in these applications, motion capture systems provide the necessary data input to animate these models. The context of this paper introduces a simple motion capture system, which is integrated into a Web-based application, thus allowing HANIM humanoids to be animated using VRML and Java. Since Web browser/VRML plugin context is commonly available on computers, the presented motion capture application is easy to use on any platform. Taking benefit of a standard language as VRML makes the exploitation of produced animation easier than other commercial application with their specific formats

ACM2000

Storage method and apparatus for random access memory using codeword storage

Harm Cronie

A memory circuit, such as an embedded DRAM array, stores information as groups of bits or data using information coding in storage and retrieval data, instead of each bit being stored separately. Write data words can be mapped to storage format words that are stored and defined by a Hadamard matrix. The storage format word is stored as charge levels in an addressable memory location. For retrieving stored data, charge levels are read from the storage cells and interpreted to a valid storage format word. Hadamard code maximal likelihood decoding can be used to derive a read data word corresponding to a previously written write data word. The write data word is then output as the result of a read of the selected addressable location, or a portion thereof. The mapping can be two or more Hadamard matrix mappings concatenated for each of a plurality of storage format words.

2016

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

EPFL2019