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Philipp Bucher - One of the best experts on this subject based on the ideXlab platform.
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MGA repository: a curated data resource for ChIP-seq and other genome annotated data
Nucleic acids research, 2017Co-Authors: René Dreos, Giovanna Ambrosini, Romain Groux, Rouayda Cavin Périer, Philipp BucherAbstract:The Mass Genome Annotation (MGA) repository is a resource designed to store published next generation sequencing data and other genome annotation data (such as gene start sites, SNPs, etc.) in a completely standardised format. Each sample has undergone local processing in order the meet the strict MGA format requirements. The original data source, the reformatting procedure and the biological characteristics of the samples are described in an accompanying Documentation File manually edited by data curators. 10 model organisms are currently represented: Homo sapiens, Mus musculus, Danio rerio, Drosophila melanogaster, Apis mellifera, Caenorhabditis elegans, Arabidopsis thaliana, Zea mays, Saccharomyces cerevisiae and Schizosaccharomyces pombe. As of today, the resource contains over 24 000 samples. In conjunction with other tools developed by our group (the ChIP-Seq and SSA servers), it allows users to carry out a great variety of analysis task with MGA samples, such as making aggregation plots and heat maps for selected genomic regions, finding peak regions, generating custom tracks for visualizing genomic features in a UCSC genome browser window, or downloading chromatin data in a table format suitable for local processing with more advanced statistical analysis software such as R. Home page: http://ccg.vital-it.ch/mga/.
Gustav Pomberger - One of the best experts on this subject based on the ideXlab platform.
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A hypertext system for literate C++ programming
Journal of Object-oriented Programming, 1992Co-Authors: Johannes Sametinger, Gustav PombergerAbstract:Programs are written to be executed by computers rather than to be read by humans. This complicates program comprehension, which plays a major role in software maintenance. Literate programming is an approach to improve program understanding by regarding programs as works of literature (see [Knu84]). In this paper we present a tool that supports literate programming with the objectoriented programming language C++. The tool is based on a hypertext system which has been developed to support program comprehension and, thus, software maintenance. An introduction of the basic hypertext system is followed by a presentation of the global structure of the Documentation. Afterwards, the user interface of the tool, its use and a sample Documentation are given. Some implementation aspects conclude the presentation. In t roduct ion Development programmers hate Documentation which, therefore, almost never is either complete or consistent. Maintenance programmers need Documentation to understand the software system they are responsible for. But they have to be satisfied with the listing, the only accurate and complete representation of the system. Understanding programs is one of the most time-consuming activities in software maintenance. By improving the availability of complete and up-to-date Documentation, we can minimize software costs considerably. When writing programs, we should not try to instruct the computer what to do, but rather we should try to tell humans what we want the computer to do. This is the main idea of literate programming (see [Knu84], [Ben86], [Lin89], [Lind89], [Wyk90]) which leads to significantly better Documentation. But as humans and computers do not speak the same language, there is a need for systems that support the idea of literate programming. The WEB System [Knu84] — the original literate programming system — offers a combination of a document formatting language for the Documentation text and a programming language for the source code (Pascal). With WEB the source code and its Documentation can be written in parallel and in a single document. The system then produces both a clearly readable program description, intended for human readers, and pure source code, intended for compilation and execution on the computer. This work was supported by Siemens AG, Munich, Germany. Several tools for literate programming have been developed so far. They support different languages like C ([Tun89], [Thi86]), Fortran [Ave90], and Smalltalk [Ree89]. Even a generator for WEB-systems is available [Ram89], which can be used to construct instances of WEB from a language description. But these systems, like the original one, are clumsy to use and assume that a program and its Documentation are written straightforward. We have based our tool on hypertext technology [Con87] to ease the navigation through a software system, both the source code and the Documentation. The tool not only supports documenting systems from scratch but also offers the opportunity to document already existing systems. The Documentation Problem Programmers always have an abstract model in their mind of what they are coding. It is important to write down these thoughts in order to make understanding easier. Writing down these thoughts is hardly ever done, for one reason because there is no place to write it. If you write it in a separate File, you do not have any connection between the source code and the corresponding Documentation File. But this connection is essential to guarantee consistent Documentation. Besides, you can hardly refer to specific parts of the code. The only way is to copy it, but this brings an unresolvable update problem. Another possiblity is to write the Documentation straight into the source code (with comments). But this again has its disadvantages: • The source code becomes illegible because of the numerous comments. • Programmers familiar with the code do not want to be annoyed by this bulky information. • The code needed to solve a problem usually is spread over several places in the source code. (This is especially true in object-oriented systems.) Literate programming tools attempt to solve these problems. However, most existing tools support the Documentation of new software. They are not very well suited to support the Documentation of already existing software. This would require the modification and restructuring of the existing source code. The literate programming tool we present in this paper supports both the Documentation of new and already existing software systems written in the object-oriented language C++. Furthermore, it offers hypertext features to comfortably navigate through the system, both the source code and the Documentation text. The Hypertext System Our Documentation tool is based on a hypertext system that was developed to support software maintenance [Sam90]. We briefly describe this maintenance tool because it is fundamental to the Documentation tool. The hypertext editor eases the process of navigating through the Files and classes of a C++ software system and helps the user to get information in a fast and easy way. To accomplish this, the Files of a C++ program are divided into little pieces of information, i.e., class definitions, method implementations and global declarations. (By global declaration we mean anything that does not belong to a class definition or to a method implementation, like preprocessor statements or global type declarations.) These little chunks of information are managed together with their interrelations. The following relations are used: • A class is contained in a File. • A class inherits from another class. • A method is contained in a File. • A method belongs to a specific class. • A method is overridden in a subclass. • A File is included by other Files. Still other relations exist based on identifiers used in a software system: • An identifier is defined in a class or method, or is global to a File. • The use of an identifier is related to a specific definition of this identifier and to other uses of the same identifier. • A comment possibly contains a short description of an identifier, e.g., the description of a class, a method, or an instance variable. Our maintenance tool offers the possibility to easily browse through the system by means of the above relations. Additionally, useful information is displayed to protect the user from getting lost in the complex information web. In order to enhance the readability of the source code, the user can define global styles for different syntactic constructs, e.g., comments, keywords. Additionally, it is possible to highlight single identifiers or identifiers defined in a certain scope. This helps the user to easily answer questions like Which global variables does this method use, and where are they used? The Documentation System The maintenance tool has been enhanced with Documentation features to a literate programming environment. The system enables its users to write Documentation during the design and coding process and offers easy access to written Documentation during the maintenance process. In the following we first describe the general structure of the Documentation built with the presented tool. Then we present the user interface and provide sample Documentation. General Structure of the Documentation We define our Documentation structure to consist of a set of Documentation chapters. These chapters are organized very similiar to classes; i.e. they are spread over several Files and a hierarchical structure exists among them. A chapter itself consists of a title, Documentation text (that is pure ASCII text) and program text (actually a link to the source code). There are two possiblities to use program text in the Documentation: 1) single identifiers 2) any text part, i.e. any number of lines of code in succession within a class definition, a method implementation and anything else in a File Single identifiers can be used right within the Documentation text, e.g.: ... With these constants we add two entries in the menu identMenu in the method CreateMenuBar of the class HyperTextDocument. ... Source code identifiers are shown boldfaced. The user can choose any font or style for these identifiers. One or more code lines are clearly separated from the Documentation text, for example: ... These menu items to copy or paste an identifier are enabled only when the source code has been parsed (i.e. ,alreadyParsed is set to TRUE) and when the current mark (cm) or the last mark copied is an identifier. The method CopiesIdent provides this information. if (cm && cm->CopiesIdent()) identMenu->EnableItem(cIdentCopy); if (GetClipMark() && GetClipMark()->CopiesIdent()) identMenu->EnableItem(cIdentPaste); Finally, whenever one of these menu items (copy or paste of identifiers) is selected by the user, the method DoMenuCommand is executed. ... Unlike the WEB system and other literate programming tools, the source code is not really intermixed with the Documentation text. This means that the source Files do not contain Documentation and the Documentation Files do not contain source code. There are only links between them and the tool merges the source code into the Documentation for browsing. User Interface The user interface concept is based on modern application frameworks and the supported concepts thereof (see [Shn86], [Wei89]). It provides a menu bar, two selection lists, an information box, and an editor window (see Fig. 1).
H. S. Das - One of the best experts on this subject based on the ideXlab platform.
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JaSTA-2: Second version of the Java Superposition T-matrix Application
Computer Physics Communications, 2017Co-Authors: Prithish Halder, H. S. DasAbstract:Abstract In this article, we announce the development of a new version of the Java Superposition T-matrix App (JaSTA-2), to study the light scattering properties of porous aggregate particles. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precision superposition T-matrix codes for multi-sphere clusters in random orientation, developed by Mackowski and Mischenko (1996). The new version consists of two options as part of the input parameters: (i) single wavelength and (ii) multiple wavelengths. The first option (which retains the applicability of older version of JaSTA) calculates the light scattering properties of aggregates of spheres for a single wavelength at a given instant of time whereas the second option can execute the code for a multiple numbers of wavelengths in a single run. JaSTA-2 provides convenient and quicker data analysis which can be used in diverse fields like Planetary Science, Atmospheric Physics, Nanoscience, etc. This version of the software is developed for Linux platform only, and it can be operated over all the cores of a processor using the multi-threading option. New version program summary Program Title: Java superposition T-matrix Application: version - 2.0 Program Files doi: http://dx.doi.org/10.17632/bbtjj8kd74.1 Licensing provisions: GPLv3 Programming language: Fortran, Java. External routines/libraries: jfreechart-1.0.14 [1] (free plotting library for java), j3d-jre-1.5.2 [2] StdDraw3D (3D visualization) Subprograms used: spline.f90, splinek.f90, wavesort.f90 Journal reference of previous version: Comput. Phys. Commun., 2014, 185, 2369 Does the new version supersede the previous version?: No. Nature of problem: Light scattering properties of cosmic dust aggregates Solution method: Java application based on Mackowski and Mishchenko’s Superposition T-Matrix code (1996). Reasons for the new version: The earlier version was mainly developed to calculate the optical properties of cosmic dust aggregates for a single wavelength in vacuum. The user had to calculate multiple times for different wavelengths to analyze the variation of different scattering parameters (e.g., phase function, polarization, the extinction efficiency, the absorption efficiency, the scattering efficiency, etc.) of aggregate particles for a range of wavelengths which was quite time-consuming. Therefore we have developed the new version of JaSTA with an ability to calculate the scattering parameters for a wide range of wavelength. In this new version, we have introduced the multi-threading option to distribute the multi-wavelength calculations to the maximum number of processing cores present in a computer. Hence the calculation time decreases considerably. Summary of revisions: Java superposition T-matrix App (JaSTA) [3] is a Java swing application developed to study the light scattering properties of cosmic dust aggregates based on the Mackowski & Mischenko’s Superposition T-matrix (STM) code [4]. This application calculates the polarization and other scattering matrix elements along with extinction, absorption, and scattering efficiencies for a single wavelength. JaSTA was solely devoted to the light scattering properties of cosmic dust aggregates. Cosmic dust includes comet dust, interplanetary dust, and interstellar dust. Many investigators studied the light scattering properties of comet dust [5]–[10], interplanetary dust [11], interstellar dust [12] using the superposition T-matrix code. JaSTA provided a much better platform for the STM code as a packaged software which can calculate light scattering properties of cosmic dust aggregates for a single wavelength in the vacuum with a click of a button and saves the results in a database so that the saved data can be re-utilized. Recently JaSTA has been used to compute the orientation-averaged scattering matrix elements for fractal aggregates of black carbon aerosols [13]. The interesting feature of the new version of JaSTA is that it can calculate the extinction efficiency at different wavelengths for a given size in a single run which is applicable in the study of interstellar extinction by aggregates at different wavelengths. To analyze the wavelength dependence of extinction one had to execute the calculation for several wavelengths by changing the wavelength and refractive indices in the input for each run in older version of JaSTA. This was very much time consuming and cumbersome. Hence this major drawback led us to rethink and re-establish JaSTA with the multi-wavelength option. JaSTA-2 is the second version of JaSTA aimed to provide the multi-wavelength facility along with the default single wavelength option. JaSTA-2 comes with some other two major updates: cubic spline interpolation of refractive index with wavelengths and multi-threading option for faster calculation. It is developed using Netbeans IDE and is available only for Linux OS. It uses jFreechart-1.0.14 java library to plot various graphs. The multi-wavelength feature will help us to extract the dependence of extinction efficiency on wavelength. Further information on the new features and applicability of JaSTA-2 are provided in the Documentation File ‘ JaSTA-2_doc.pdf ’, and ‘ readme.txt ’ File which are available in the software package. [1] http://www.jfree.org/index.html [2] https://java3d.java.net/ [3] P. Halder, A. Chakraborty, P. Deb Roy & H.S. Das, Computer Physics Communications, 185 (2014) 2369-2379. [4] D.W. Mackowski & M.I. Mischenko, J. Opt. Soc. Am. Am., 13 (1996) 2266-2278. [5] H. Kimura, L. Kolokolova & I. Mann, A&A, 407 (2003) L5-L8. [6] H. Kimura, L. Kolokolova & I. Mann, A&A, 449 (2006) 1243-1254. [7] H.S. Das, S.R. Das, T. Paul, A. Suklabaidya & A.K. Sen, MNRAS, 389 (2008) 787-791. [8] H.S. Das, S.R. Das & A.K Sen, MNRAS, 390 (2008) 1195-1199. [9] H.S. Das, A. Suklabaidya, S. Datta Majumder & A.K. Sen, Research in A&A, 10 (2010) 355-362 [10] H.S. Das, D. Paul, A. Suklabaidya & A.K. Sen, MNRAS, 416 (2011) 94-100. [11] J. Lasue, A.C. Levasseur-Regourd, N. Fray & H. Cottin, A&A, 473 (2007) 641-649. [12] M. A. Iati, A. Giusto, R. Saija, F. Borghese, P. Denti, C. Cecchi-Pestellini & S. Aielo, ApJ, 615 (2004), 286. [13] A. Pandey & R. K. Chakrabarty, Optics Letters, 41 (2016) 3351-3354.
Norbert Grobe - One of the best experts on this subject based on the ideXlab platform.
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A retrospective review of diagnosis and treatment modalities of neuroendocrine tumors (excluding primary lung cancer) in 10 oncological institutions of the East German Study Group of Hematology and Oncology (OSHO), 2010–2012
Journal of Cancer Research and Clinical Oncology, 2015Co-Authors: Georg Maschmeyer, Lars-olof Mügge, Dietrich Kämpfe, Ute Kreibich, Stephan Wilhelm, Michael Aßmann, Maik Schwarz, Christoph Kahl, Susanne Köhler, Norbert GrobeAbstract:Rationale There is a paucity of data on the incidence of neuroendocrine tumors (NET) outside pulmonary primaries and on treatment modalities applied to patients with NET in clinical practice. Only very little therapeutic progress has been made with respect to response and overall survival, particularly among patients with poorly differentiated, WHO grade 3 neuroendocrine carcinomas (G3-NEC). We sought to document the incidence and treatment modalities in patients with NET/NEC within a period of 2 years. Methods We conducted a retrospective data analysis using a simple Documentation File to be completed in written form or electronically, including localization, WHO grading, treatment modalities, and specific therapeutic regimens applied. Primary lung cancer was excluded. The time period to be covered was 2010 through 2012. Individual patient data such as names or age were not documented, so that no ethics committee approval was required. Results Ten different hospital- or practice-based institutions contributed their data. One to 35 patients were documented per institution, summing up to 149 patients with 154 tumor localizations. Midgut ( n = 46), foregut ( n = 42), hindgut ( n = 17), lung ( n = 9), bladder ( n = 8), unknown primary ( n = 11), and other including prostate and liver ( n = 21) were documented as tumor sites. Histological gradings were G1 ( n = 71), G2 ( n = 27), G3 ( n = 34), undifferentiated “G4” ( n = 4), and not specified ( n = 13). Treatment modalities were surgical resection ( n = 102), chemotherapy ( n = 49), somatostatin analogs ( n = 39), radiotherapy ( n = 22), receptor-directed radionuclide therapy ( n = 12), and systemic tyrosine kinase inhibition ( n = 5). Chemotherapy was given to patients not only with G3-NEC ( n = 31), but also with G2 ( n = 12) and G1 NET ( n = 7). Somatostatin analogs as well as receptor-directed radionuclides were applied to patients throughout all gradings. Conclusions NET and NEC are not very rare tumor entities, but are diagnosed with very different frequencies, possibly depending upon the alertness of pathologists and clinicians. Chemotherapy, receptor-directed radionuclide application, and somatostatin analog therapy are applied without a clear correlation to different histologic gradings. Diagnostic and therapeutic progress in the field of NETs/carcinomas is urgently needed.
René Dreos - One of the best experts on this subject based on the ideXlab platform.
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MGA repository: a curated data resource for ChIP-seq and other genome annotated data
Nucleic acids research, 2017Co-Authors: René Dreos, Giovanna Ambrosini, Romain Groux, Rouayda Cavin Périer, Philipp BucherAbstract:The Mass Genome Annotation (MGA) repository is a resource designed to store published next generation sequencing data and other genome annotation data (such as gene start sites, SNPs, etc.) in a completely standardised format. Each sample has undergone local processing in order the meet the strict MGA format requirements. The original data source, the reformatting procedure and the biological characteristics of the samples are described in an accompanying Documentation File manually edited by data curators. 10 model organisms are currently represented: Homo sapiens, Mus musculus, Danio rerio, Drosophila melanogaster, Apis mellifera, Caenorhabditis elegans, Arabidopsis thaliana, Zea mays, Saccharomyces cerevisiae and Schizosaccharomyces pombe. As of today, the resource contains over 24 000 samples. In conjunction with other tools developed by our group (the ChIP-Seq and SSA servers), it allows users to carry out a great variety of analysis task with MGA samples, such as making aggregation plots and heat maps for selected genomic regions, finding peak regions, generating custom tracks for visualizing genomic features in a UCSC genome browser window, or downloading chromatin data in a table format suitable for local processing with more advanced statistical analysis software such as R. Home page: http://ccg.vital-it.ch/mga/.