Search Results for "libamd.so.1"
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Showing 47 open source projects for "libamd.so.1"
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Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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Host LLMs in Production With On-Demand GPUsDeploy your model, get an endpoint, pay only for compute time. No GPU provisioning or infrastructure management required.
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luscus
molecular editor and viewer
...The program is developed as a graphical interface for MOLCAS program package, however it's adaptive nature makes possible using luscus with other computational program packages and chemical formats. If you use this program, please cite: G. Kovačević, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z -
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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Eleana
Program for the analysis of spectroscopic data, in particular EPR(ESR)
Eleana is a program for manipulating, modifying and analyzing various spectroscopic data, in particular electron paramagnetic resonance spectra. It allows you to import data from Bruker spectrometers such as Elexsys or EMX and data from any ASCII file or imported from the clipboard. The program is under constant development, but already has many functions implemented for spectral analysis. Some of the basic functions include: baseline corrections, filtering, spectral clipping, integration /... -
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MAF
Bash Framework to combine many preprocessing and alignment tools
DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom parameter combinations if in-depth analysis is necessary or advised in e.g. low read rate situations. ... -
Secure File Transfer for Windows with Cerberus by RedwoodCerberus supports unlimited users and connections on a single IP, with built-in encryption, 2FA, and a browser-based web client — all deployable in under 15 minutes with a 25-day free trial.
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DEEP
Differential Evolution Entirely Parallel Method
The Differential Evolution, introduced in 1995 by Storn and Price, considers the population, that is divided into branches, one per computational node. The Differential Evolution Entirely Parallel method takes into account the individual age, that is defined as the number of iterations the individual survived without changes. The introduced improvements are: (I) allow several oldest individuals to be overwritten by the same number of best ones in the population, (II) new selection rule uses several objective functions in offspring evaluation. ... -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
...Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. No programming skills are required to use kSNP4 Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760 Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271 -
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AstroBioTools
Adaptive analysis of amino acid alphabets
...Ilardo, M., Bose, R., Meringer, M., Rasulev, B., Grefenstette, N., Stephenson, J., Freeland, S., Gillams, R. J. , Butch C. J., & Cleaves, H. J. (2019). Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets. Scientific reports, 9(1), 1-9. Example program calls: ./CliAdaptiveAnalysis -i data/Table1913Aa4Prop.txt -n 100000 ./CliAdaptiveAnalysis -i data/Table1913Aa4Prop.txt -n 100000000 -v -
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...More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be reimplemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.
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TVscript
Exploration of the removal of count variable transcripts.
> See TVscript wiki: https://sourceforge.net/p/tvscript/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: (See wiki) 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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qmol
A simple molecular weight calculator
qmol is a simple molecular weight calculator, available for Linux and Windows, derived from Tomislav Gountchev's KMol. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %). See the features list below for more details or consult the wiki page: https://sourceforge.net/p/qmol/wiki/Home/. For Windows binary and source code see the files section:... -
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sciNote
Open source electronic lab notebook (ELN) for scientists
sciNote is an open source electronic lab notebook (ELN) that helps you manage your laboratory work and stores all your experimental data in one place. sciNote is specifically designed for life science students, researchers, lab technicians and group leaders. -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. ... -
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The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
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PF_HP
Prediction of proteinfolding in 2D HP model
Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings). Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die Proteinfaltung. Spende einen Cappuccino: Bitcoin: 1HqrdnfQgi9B4LW8UEvLAwh7X5gXPCoQ5B Litecoin: Lbo2jxD85ymyq5167r7yFVZkEr73F2h44B Paypal: paypal.me/GerritLeder Credits ====== Principle Investigator -------------------------- Gerrit Leder: protein folding algorithm design and testing, and initial implementation in Eiffel. ... -
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This package includes a collection of MATLAB files which are designed to: 1. Given a calibration scan of the image of a point emitter with an engineered point spread function (PSF), 2. Perform a phase retrieval algorithm based on maximum likelihood estimation (MLE) of a phase aberration term which is added to the theoretical pupil function of the imaging system. 3. Use the phase-retrieved pupil function to perform single-emitter localization.
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
Minimum spanning tree (MST) algorithms can generate multiple, equally-minimal, MSTs but MST programs typically report only one, arbitrarily chosen MST. Similarly, most MST programs do not provide statistical metrics to support the credibility of the MSTs that they estimate. MSTgold estimates the number of alternative MSTs, reports up to a user-determined number of those trees, reports a consensus tree, and implements a bootstrapping metric to assess the reliability of alternate MST solutions. ... -
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
...Disctretization leads to generalized eigenvalue problem, which is solved by procedures from LAPACK libraries. The program is implemented in C++, it runs as a single thread. The implemented algorithm is described in the following papers: 1. Z. Romanowski, "Adaptive solver of a Kohn-Sham equation for an atom", Modelling Simul. Mater. Sci. Eng. vol. 17, 045001 (2009) 2. Z. Romanowski, "Application of h-adaptive, high order finite element method to solve radial Schrödinger equation", Molecular Physics, vol. 107, pp. 1339-1348 (2009). Further questions: romz@wp.pl -
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RSchr-5
Solves one-electron Schrödinger equation, with SLEPc and PETSc
RSchr-5 calculates the smallest eigenvalues of the one-electron Schrödinger equation. The solved problem is defined on the finite domain, which is a box. The problem is solved with the zero Dirichlet boundary conditions. The implemented algorithm uses Finite Element Method with B-splines as basis functions. Disctretization leads to generalized eigenvalue problem. Program RSchr-5 solves the generalized eigenvalue problem by algorithms implemented in SLEPc amd PETSc libraries. ... -
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time. -
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Reference implementation of the Systems Biology Graphical Notation: map exchange format and library handling import/export and validation. Resource of the libSBGN project have been migrated from SourceForge to GitHub. Latest changes can be found on GitHub now. The code repository can be found here now https://github.com/sbgn/libsbgn The files (releases) can be found here now https://github.com/sbgn/libsbgn/releases The bugs and features (issues) can be found here...
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Nancy_EX
Quantum Chemistry: Excited States Topology
...The code is intended to postprocess Gaussian 03 and 09 outputs. Important Note: A new release with better compilation option has been released on November the 9th 2015. We strongly advise to use this one since the previous option may have led to some unexpected bugs. -
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HYBRYD
Library written in C with Python API for IPv6 networking
This project is a rewritten of an initial project that I've called GLUE and created in 2005. I'm trying to readapt it for Python 2.7.3 and GCC 4.6.3 The library has to be build as a simple Python extension using >python setup.py install and allows to create different kind of servers, clients or hybryds (clients-servers) over (TCP/UDP) using the Ipv6 Protocol. The architecture of the code is based on brain architecture. Will put an IPv6 adress active available as soon as... -
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A toolkit in C++ and python to process both experimental and simulation data of colloidal particles. Includes among others * a multiscale particle tracking algorithm [1] whose C++ implementation is optimised for 3D confocal data. Python implementation is more versatile (2D and 3D data). * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H. A novel particle tracking method with individual particle size measurement and its application to ordering in glassy hard sphere colloids. ...
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
.... (2) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan 1;42(1):D756-63. (3) Cock PJ et al. Bioinformatics (2009) (4) Cokelaer et al, Bioinformatics (2013)