The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy, which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project.

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The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package

Lysine acetylation is a reversible posttranslational modification of proteins and plays a key role in regulating gene expression. Technological limitations have so far prevented a global analysis of lysine acetylation's cellular roles. We used high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 proteins and quantified acetylation changes in response to the deacetylase inhibitors suberoylanilide hydroxamic acid and MS-275. Lysine acetylation preferentially targets large macromolecular complexes involved in diverse cellular processes, such as chromatin remodeling, cell cycle, splicing, nuclear transport, and actin nucleation. Acetylation impaired phosphorylation-dependent interactions of 14-3-3 and regulated the yeast cyclin-dependent kinase Cdc28. Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications.

https://science.sciencemag.org/content/suppl/2009/07/16/1175371.DC1/Choudhary-SOM.pdf

Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

(Abridged) The Large Area Telescope (Fermi/LAT, hereafter LAT), the primary instrument on the Fermi Gamma-ray Space Telescope (Fermi) mission, is an imaging, wide field-of-view, high-energy gamma-ray telescope, covering the energy range from below 20 MeV to more than 300 GeV. This paper describes the LAT, its pre-flight expected performance, and summarizes the key science objectives that will be addressed. On-orbit performance will be presented in detail in a subsequent paper. The LAT is a pair-conversion telescope with a precision tracker and calorimeter, each consisting of a 4x4 array of 16 modules, a segmented anticoincidence detector that covers the tracker array, and a programmable trigger and data acquisition system. Each tracker module has a vertical stack of 18 x,y tracking planes, including two layers (x and y) of single-sided silicon strip detectors and high-Z converter material (tungsten) per tray. Every calorimeter module has 96 CsI(Tl) crystals, arranged in an 8 layer hodoscopic configuration with a total depth of 8.6 radiation lengths. The aspect ratio of the tracker (height/width) is 0.4 allowing a large field-of-view (2.4 sr). Data obtained with the LAT are intended to (i) permit rapid notification of high-energy gamma-ray bursts (GRBs) and transients and facilitate monitoring of variable sources, (ii) yield an extensive catalog of several thousand high-energy sources obtained from an all-sky survey, (iii) measure spectra from 20 MeV to more than 50 GeV for several hundred sources, (iv) localize point sources to 0.3 - 2 arc minutes, (v) map and obtain spectra of extended sources such as SNRs, molecular clouds, and nearby galaxies, (vi) measure the diffuse isotropic gamma-ray background up to TeV energies, and (vii) explore the discovery space for dark matter.

The Large Area Telescope on the Fermi Gamma-ray Space Telescope Mission

Wavelets were developed independently by mathematicians, quantum physicists, electrical engineers and geologists, but collaborations among these fields during the last decade have led to new and varied applications. What are wavelets, and why might they be useful to you? The fundamental idea behind wavelets is to analyze according to scale. Indeed, some researchers feel that using wavelets means adopting a whole new mind-set or perspective in processing data. Wavelets are functions that satisfy certain mathematical requirements and are used in representing data or other functions. Most of the basic wavelet theory has now been done. The mathematics have been worked out in excruciating detail, and wavelet theory is now in the refinement stage. This involves generalizing and extending wavelets, such as in extending wavelet packet techniques. The future of wavelets lies in the as-yet uncharted territory of applications. Wavelet techniques have not been thoroughly worked out in such applications as practical data analysis, where, for example, discretely sampled time-series data might need to be analyzed. Such applications offer exciting avenues for exploration. >

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An introduction to wavelets

We review the properties and behavior of 20 X-ray binaries that contain a dynamically-confirmed black hole, 17 of which are transient systems. During the past decade, many of these transien...

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X-Ray Properties of Black-Hole Binaries

Alanna was one of the most important pioneers in the development of not just sophisticated algorithms for analyzing astronomical data but more importantly an overall viewpoint emphasizing the use of statistically sound principles in place of blind application of cook-book recipes, or black boxes. I will outline some of the threads of this viewpoint, emphasizing time series data, with a focus on the importance of these developments for the Age of Digital Astronomy that we are entering.

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Alanna Conners and the Origins of Principled Data Analysis

I describe an extension, to higher dimensions, of the Bayesian Blocks algorithm for estimating signals in noisy time series data [17,18]. We seek the partition of the data space with the maximum posterior for a model consisting of a homogeneous Poisson process in each partition element. Model Mn, attributing the data within region n of the data space to a Poisson process with a fixed event rate λn, has a global posterior depending on only N, the number of data points in the region, and V, its volume: P(Mn)=Φ(N,V)=Γ(N+1)Γ(V−N+1)/Γ(V+2)=N!(V−N)!/(V+1)!. (1) Note that λn does not appear, since it has been marginalized, using a flat, improper prior. Other priors yield similar formulas. This expression is valid for a data space of any dimension. Suppose two regions, described by N1, V1 and N2, V2, are candidates for being merged into one. The Bayes merge factor, giving the posterior ratio for merged and not merged, respectively, is: P=Φ(N1+N2,V1+V2)/Φ(N1,V1)Φ(N2,V2).  (2) Then collect data points into blocks w...

Bayesian blocks in two or more dimensions: Image segmentation and cluster analysis

We are witnessing the birth of a new observational science: the discovery and characterization of extrasolar planetary systems. In the past five years, over 70 extrasolar planets have been discovered by precision Doppler surveys, most by members of this SIM team. We are using the data base of information gleaned from our Doppler survey to choose the best targets for a new SIN planet search. In the same way that our Doppler database now serves SIM, our team will return a reconnaissance database to focus Terrestrial Planet Finder (TPF) into a more productive, efficient mission.

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Discovery of Planetary Systems With SIM

The advent of the Space Station Program has provided an unexpected opportunity for the Astrometric Telescope Facility (ATF) study program by providing a potential long-duration on-orbit serviceable platform It required a concept change for ATF from a free-flyer observatory to a Space-Station-based Observatory The program was sent in this new direction at the start of fiscal year 1985, and program plans including study schedules and science and technical requirements are being revised and defined The facility is designed to be versatile and capable of fulfilling the primary goal of planet detection, and to be highly useful for other astrophysics observations Basically the ATF observing program is a long-duration plan requiring repetitive observations of single stars over a one to two decade period These repetitive observations are needed to provide data necessary to conclusively determine the existence (or nonexistence) of planets of the Uranus and Neptune class in extrasolar planetary systems

Jeffrey D. Scargle

Papers

Alanna Conners and the Origins of Principled Data Analysis

Bayesian blocks in two or more dimensions: Image segmentation and cluster analysis

Discovery of Planetary Systems With SIM

Astrometric Telescope Facility - Status report

The Far Infrared Spectrum of Jupiter