scholarly journals Two Independent and Highly Efficient Open Source TKF91 Implementations

2015 ◽  
Author(s):  
Nikolai Baudis ◽  
Pierre Barbera ◽  
Sebastian Graf ◽  
Sarah Lutteropp ◽  
Daniel Opitz ◽  
...  
Keyword(s):  
Open Source ◽  
Science Department ◽  
Teacher Experiences ◽  
Source Codes ◽  
Student Teams ◽  
Master Level ◽  
Alignment Model ◽  
Institute Of Technology ◽  
Karlsruhe Institute ◽  
Statistical Alignment

In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by Thorne, Kishino, and Felsenstein in 1991. This paper has two parts. In the educational part, we cover teaching issues regarding the setup of the course and the practical and summarize student and teacher experiences. In the scientific part, the two student teams (Team I: Nikolai, Sebastian, Daniel; Team II: Sarah, Pierre) present their solutions for implementing efficient and numerically stable implementations of the TKF91 algorithm. The two teams worked independently on implementing the same algorithm. Hence, since the implementations yield identical results -with slight numerical deviations- we are confident that the implementations are correct. We describe the optimizations applied and make them available as open-source codes in the hope that our findings and software will be useful to the community as well as for similar programming practicals at other universities.

scholarly journals Arduino based platform for process control learning

2020 ◽  
Vol 6 (5) ◽  
pp. 0585-0593
Author(s):  
Bruna Couto Molinar Henrique ◽  
Leonardo Couto Molinar Henrique ◽  
Humberto Molinar Henrique
Keyword(s):  
Open Source ◽  
Real Time ◽  
Low Cost ◽  
Control Unit ◽  
Absolute Error ◽  
Internal Model Control ◽  
Pid Controllers ◽  
Experimental Unit ◽  
Source Codes ◽  
Model Control

This work deals with implementation of an experimental flowrate control unit using free and low-cost hardware and software. The open-source software Processing was used to develop the source codes and user graphical interface and the open-source electronic prototyping platform Arduino was used to acquire data from an experimental unit. Work presents descriptions of the experimental setup, the real-time PID controllers used and theoretical/conceptual issues of Arduino. PID controllers based on internal model control, minimization of the integral of time-weighted absolute error, Ziegler-Nichols, and others were tuned for setpoint and load changes and real-time runs were carried out in order to make real-time use of  control theory learned in academy. Results showed the developed platform proved to be suitable for use in experimental setups allowing users compare their ideas and expectations with the experimental evidence in a real and low-cost fashion. In addition, the instrumentation is simple to configure with acceptable level noise and particularly useful for control/automation learning with educational purposes.

scholarly journals A Systematic Comparison of Various Statistical Alignment Models

2003 ◽  
Vol 29 (1) ◽  
pp. 19-51 ◽  
Author(s):  
Franz Josef Och ◽  
Hermann Ney
Keyword(s):  
Training Algorithm ◽  
Dice Coefficient ◽  
Design Decisions ◽  
First Order ◽  
Model Yield ◽  
Alignment System ◽  
Word Alignments ◽  
Alignment Model ◽  
Statistical Alignment

We present and compare various methods for computing word alignments using statistical or heuristic models. We consider the five alignment models presented in Brown, Della Pietra, Della Pietra, and Mercer (1993), the hidden Markov alignment model, smoothing techniques, and refinements. These statistical models are compared with two heuristic models based on the Dice coefficient. We present different methods for combining word alignments to perform a symmetrization of directed statistical alignment models. As evaluation criterion, we use the quality of the resulting Viterbi alignment compared to a manually produced reference alignment. We evaluate the models on the German-English Verbmobil task and the French-English Hansards task. We perform a detailed analysis of various design decisions of our statistical alignment system and evaluate these on training corpora of various sizes. An important result is that refined alignment models with a first-order dependence and a fertility model yield significantly better results than simple heuristic models. In the Appendix, we present an efficient training algorithm for the alignment models presented.

Optimization Scenarios for Open Source Software Used in E-Learning Activities

2018 ◽  
pp. 102-123
Author(s):  
Utku Köse
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Learning Experience ◽  
Learning Activities ◽  
Machine Learning Techniques ◽  
Software Systems ◽  
Source Codes ◽  
E Learning ◽  
Additional Costs ◽  
Teaching Learning

Using open software in e-learning application is one of the most popular ways of improving effectiveness of e-learning-based processes without thinking about additional costs and even focusing on modifying the software according to needs. Because of that, it is important to have an idea about what is needed while using an e-learning-oriented open software system and how to deal with its source codes. At this point, it is a good option to add some additional features and functions to make the open source software more intelligent and practical to make both teaching-learning experiences during e-learning processes. In this context, the objective of this chapter is to discuss some possible applications of artificial intelligence to include optimization processes within open source software systems used in e-learning activities. In detail, the chapter focuses more on using swarm intelligence and machine learning techniques for this aim and expresses some theoretical views for improving the effectiveness of such software for a better e-learning experience.

scholarly journals Integrated Computational Pipeline for Single-Cell Genomic Profiling

2020 ◽  
pp. 464-471 ◽  
Author(s):  
Lubomir Chorbadjiev ◽  
Jude Kendall ◽  
Joan Alexander ◽  
Viacheslav Zhygulin ◽  
Junyan Song ◽  
...  
Keyword(s):  
Single Cell ◽  
Open Source ◽  
Copy Number ◽  
Cancer Diagnostics ◽  
Massachusetts Institute Of Technology ◽  
Computational Pipeline ◽  
Single Cell Genomics ◽  
Single Nucleus ◽  
Institute Of Technology ◽  
Cell Genome

PURPOSE Copy-number profiling of multiple individual cells from sparse sequencing may be used to reveal a detailed picture of genomic heterogeneity and clonal organization in a tissue biopsy specimen. We sought to provide a comprehensive computational pipeline for single-cell genomics, to facilitate adoption of this molecular technology for basic and translational research. MATERIALS AND METHODS The pipeline comprises software tools programmed in Python and in R and depends on Bowtie, HISAT2, Matplotlib, and Qt. It is installed and used with Anaconda. RESULTS Here we describe a complete pipeline for sparse single-cell genomic data, encompassing all steps of single-nucleus DNA copy-number profiling, from raw sequence processing to clonal structure analysis and visualization. For the latter, a specialized graphical user interface termed the single-cell genome viewer (SCGV) is provided. With applications to cancer diagnostics in mind, the SCGV allows for zooming and linkage to the University of California at Santa Cruz Genome Browser from each of the multiple integrated views of single-cell copy-number profiles. The latter can be organized by clonal substructure or by any of the associated metadata such as anatomic location and histologic characterization. CONCLUSION The pipeline is available as open-source software for Linux and OS X. Its modular structure, extensive documentation, and ease of deployment using Anaconda facilitate its adoption by researchers and practitioners of single-cell genomics. With open-source availability and Massachusetts Institute of Technology licensing, it provides a basis for additional development by the cancer bioinformatics community.

Transplantation of U-Boot on NAND Flash Based on S3C2440 Processor

2014 ◽  
Vol 716-717 ◽  
pp. 1199-1202
Author(s):  
Peng Zhang ◽  
Zhi Wei Peng ◽  
Jian Wei Lv ◽  
Zhao Yu Ding
Keyword(s):  
Operating System ◽  
Open Source ◽  
High Reliability ◽  
Main Task ◽  
Nand Flash ◽  
Embedded Operating System ◽  
Source Codes ◽  
Start Up ◽  
Target Platform

The main task of bootloader is to copy the kernel image to RAM , and then jump to the entrance of the kernel to run the operating system . It is the first-running code when the system is powered on . U-boot , with its open-source codes , supporting for varieties of embedded operating system kernel , high reliability and stability , has been in the mainstream of bootloader . However , it has not yet provided the original support for the S3C2440 processor , neither does its NAND flash . This paper analyzes two flashes in reference to the corresponding start-up mode , and introduces the U-boot start-up procedures briefly and figures out the major steps of transplanting U-boot to the target platform . U-boot was transplanted successfully .

scholarly journals KIT coaxial gyrotron development: from ITER toward DEMO

2018 ◽  
Vol 10 (5-6) ◽  
pp. 547-555 ◽  
Author(s):  
S. Ruess ◽  
K. A. Avramidis ◽  
M. Fuchs ◽  
G. Gantenbein ◽  
Z. Ioannidis ◽  
...  
Keyword(s):  
Output Power ◽  
Electron Cyclotron Resonance ◽  
Short Pulse ◽  
Electron Cyclotron Resonance Heating ◽  
Major Step ◽  
Coaxial Cavity ◽  
Design And Manufacturing ◽  
Institute Of Technology ◽  
Coaxial Gyrotron ◽  
Karlsruhe Institute

Karlsruhe Institute of Technology (KIT) is doing research and development in the field of megawatt-class radio frequency (RF) sources (gyrotrons) for the Electron Cyclotron Resonance Heating (ECRH) systems of the International Thermonuclear Experimental Reactor (ITER) and the DEMOnstration Fusion Power Plant that will follow ITER. In the focus is the development and verification of the European coaxial-cavity gyrotron technology which shall lead to gyrotrons operating at an RF output power significantly larger than 1 MW CW and at an operating frequency above 200 GHz. A major step into that direction is the final verification of the European 170 GHz 2 MW coaxial-cavity pre-prototype at longer pulses up to 1 s. It bases on the upgrade of an already existing highly modular short-pulse (ms-range) pre-prototype. That pre-prototype has shown a world record output power of 2.2 MW already. This paper summarizes briefly the already achieved experimental results using the short-pulse pre-prototype and discusses in detail the design and manufacturing process of the upgrade of the pre-prototype toward longer pulses up to 1 s.

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