Development of data representation standards by the human proteome organization proteomics standards initiative.

OBJECTIVE: To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI's evolution, and future directions and synergies for the group. MATERIALS AND METHODS: The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release. RESULTS: We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info

FACT - Long-term stability and observations during strong Moon light

The First G-APD Cherenkov Telescope (FACT) is the first Cherenkov telescope equipped with a camera made of silicon photon detectors (G-APD aka. SiPM). Since October 2011, it is regularly taking data on the Canary Island of La Palma. G-APDs are ideal detectors for Cherenkov telescopes as they are robust and stable. Furthermore, the insensitivity of G-APDs towards strong ambient light allows to conduct observations during bright Moon and twilight. This gain in observation time is essential for the long-term monitoring of bright TeV blazars. During the commissioning phase, hundreds of hours of data (including data from the the Crab Nebula) were taken in order to understand the performance and sensitivity of the instrument. The data cover a wide range of observation conditions including different weather conditions, different zenith angles and different light conditions (ranging from dark night to direct full Moon). We use a new parmetrisation of the Moon light background to enhance our scheduling and to monitor the atmosphere. With the data from 1.5 years, the long-term stability and the performance of the camera during Moon light is studied and compared to that achieved with photomultiplier tubes so far.Comment: 3 pages, 3 figures, FACT Contribution to the 33rd International Cosmic Ray Conference (ICRC), Rio de Janeir

FACT - Threshold prediction for higher duty cycle and improved scheduling

The First G-APD Cherenkov telescope (FACT) is the first telescope using silicon photon detectors (G-APD aka. SiPM). The use of Silicon devices promise a higher photon detection efficiency, more robustness and higher precision than photo-multiplier tubes. Being operated during different light-conditions, the threshold settings of a Cherenkov telescope have to be adapted to feature the lowest possible threshold but also an efficient suppression of triggers from night-sky background photons. Usually this threshold is set either by experience or a mini-ratescan. Since the measured current through the sensors is directly correlated with the noise level, the current can be used to set the best threshold at any time. Due to the correlation between the physical threshold and the final energy threshold, the current can also be used as a measure for the energy threshold of any observation. This presentation introduces a method which uses the properties of the moon and the source position to predict the currents and the corresponding energy threshold for every upcoming observation allowing to adapt the observation schedule accordingly

FACT - Long-term Monitoring of Bright TeV-Blazars

Since October 2011, the First G-APD Cherenkov Telescope (FACT) is operated successfully on the Canary Island of La Palma. Apart from the proof of principle for the use of G-APDs in Cherenkov telescopes, the major goal of the project is the dedicated long-term monitoring of a small sample of bright TeV blazars. The unique properties of G-APDs permit stable observations also during strong moon light. Thus a superior sampling density is provided on time scales at which the blazar variability amplitudes are expected to be largest, as exemplified by the spectacular variations of Mrk 501 observed in June 2012. While still in commissioning, FACT monitored bright blazars like Mrk 421 and Mrk 501 during the past 1.5 years so far. Preliminary results including the Mrk 501 flare from June 2012 will be presented.Comment: 4 pages, 4 figures, presented at the 33rd ICRC (2013

FACT - How stable are the silicon photon detectors?

The First G-APD Cherenkov telescope (FACT) is the first telescope using silicon photon detectors (G-APD aka. SiPM). The use of Silicon devices promise a higher photon detection efficiency, more robustness and higher precision than photo-multiplier tubes. Since the properties of G-APDs depend on auxiliary parameters like temperature, a feedback system adapting the applied voltage accordingly is mandatory. In this presentation, the feedback system, developed and in operation for FACT, is presented. Using the extraction of a single photon-equivalent (pe) spectrum as a reference, it can be proven that the sensors can be operated with very high precision. The extraction of the single-pe, its spectrum up to 10\,pe, its properties and their precision, as well as their long-term behavior during operation are discussed. As a by product a single pulse template is obtained. It is shown that with the presented method, an additional external calibration device can be omitted. The presented method is essential for the application of G-APDs in future projects in Cherenkov astronomy and is supposed to result in a more stable and precise operation than possible with photo-multiplier tubes

Development of data representation standards by the human proteome organization proteomics standards initiative

Objective To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI's evolution, and future directions and synergies for the group. Materials and Methods The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release. Results We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community. Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.inf

Calibration and performance of the photon sensor response of FACT -- The First G-APD Cherenkov telescope

The First G-APD Cherenkov Telescope (FACT) is the first in-operation test of the performance of silicon photo detectors in Cherenkov Astronomy. For more than two years it is operated on La Palma, Canary Islands (Spain), for the purpose of long-term monitoring of astrophysical sources. For this, the performance of the photo detectors is crucial and therefore has been studied in great detail. Special care has been taken for their temperature and voltage dependence implementing a correction method to keep their properties stable. Several measurements have been carried out to monitor the performance. The measurements and their results are shown, demonstrating the stability of the gain below the percent level. The resulting stability of the whole system is discussed, nicely demonstrating that silicon photo detectors are perfectly suited for the usage in Cherenkov telescopes, especially for long-term monitoring purpose

A standardized framing for reporting protein identifications in mzIdentML 1.2

Inferring which protein species have been detected in bottom-up proteomics experiments has been a challenging problem for which solutions have been maturing over the past decade. While many inference approaches now function well in isolation, comparing and reconciling the results generated across different tools remains difficult. It presently stands as one of the greatest barriers in collaborative efforts such as the Human Proteome Project and public repositories such as the PRoteomics IDEntifications (PRIDE) database. Here we present a framework for reporting protein identifications that seeks to improve capabilities for comparing results generated by different inference tools. This framework standardizes the terminology for describing protein identification results, associated with the HUPO-Proteomics Standards Initiative (PSI) mzIdentML standard, while still allowing for differing methodologies to reach that final state. It is proposed that developers of software for reporting identification results will adopt this terminology in their outputs. While the new terminology does not require any changes to the core mzIdentML model, it represents a significant change in practice, and, as such, the rules will be released via a new version of the mzIdentML specification (version 1.2) so that consumers of files are able to determine whether the new guidelines have been adopted by export software

FACT -- Operation of the First G-APD Cherenkov Telescope

Since more than two years, the First G-APD Cherenkov Telescope (FACT) is operating successfully at the Canary Island of La Palma. Apart from its purpose to serve as a monitoring facility for the brightest TeV blazars, it was built as a major step to establish solid state photon counters as detectors in Cherenkov astronomy. The camera of the First G-APD Cherenkov Telesope comprises 1440 Geiger-mode avalanche photo diodes (G-APD aka. MPPC or SiPM) for photon detection. Since properties as the gain of G-APDs depend on temperature and the applied voltage, a real-time feedback system has been developed and implemented. To correct for the change introduced by temperature, several sensors have been placed close to the photon detectors. Their read out is used to calculate a corresponding voltage offset. In addition to temperature changes, changing current introduces a voltage drop in the supporting resistor network. To correct changes in the voltage drop introduced by varying photon flux from the night-sky background, the current is measured and the voltage drop calculated. To check the stability of the G-APD properties, dark count spectra with high statistics have been taken under different environmental conditions and been evaluated. The maximum data rate delivered by the camera is about 240 MB/s. The recorded data, which can exceed 1 TB in a moonless night, is compressed in real-time with a proprietary loss-less algorithm. The performance is better than gzip by almost a factor of two in compression ratio and speed. In total, two to three CPU cores are needed for data taking. In parallel, a quick-look analysis of the recently recorded data is executed on a second machine. Its result is publicly available within a few minutes after the data were taken. [...]Comment: 19th IEEE Real-Time Conference, Nara, Japan (2014

FACT -- The G-APD revolution in Cherenkov astronomy

Since two years, the FACT telescope is operating on the Canary Island of La Palma. Apart from its purpose to serve as a monitoring facility for the brightest TeV blazars, it was built as a major step to establish solid state photon counters as detectors in Cherenkov astronomy. The camera of the First G-APD Cherenkov Telesope comprises 1440 Geiger-mode avalanche photo diodes (G-APD), equipped with solid light guides to increase the effective light collection area of each sensor. Since no sense-line is available, a special challenge is to keep the applied voltage stable although the current drawn by the G-APD depends on the flux of night-sky background photons significantly varying with ambient light conditions. Methods have been developed to keep the temperature and voltage dependent response of the G-APDs stable during operation. As a cross-check, dark count spectra with high statistics have been taken under different environmental conditions. In this presentation, the project, the developed methods and the experience from two years of operation of the first G-APD based camera in Cherenkov astronomy under changing environmental conditions will be presented.Comment: Proceedings of the Nuclear Science Symposium and Medical Imaging Conference (IEEE-NSS/MIC), 201