Search Results for "asn.1 to java compiler"
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Showing 113 open source projects for "asn.1 to java compiler"
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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other... -
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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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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
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The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN.
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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR....
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BD-Func
Bidirectional Functional Enrichment of Gene Expression Data
BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159 -
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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/ -
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LoopMatcher
Find sequence-specific stem-loops in FASTA and GenBank files.
LoopMatcher is a bioinformatics tool that searches for hairpin structures in cDNA / mRNA sequences (in FASTA, GenBank or Vienna format) with specific consensus sequences in the loop. It uses RNAfold to predict sequence structure and UShuffle to generate random sequences with a defined k nucleotide frequency. Also, sequences in GenBank format can be downloaded directly from NCBI using the NCBI access ID. Requirements JAVA Runtime 8. It's highly recommended to have a multicore processor... -
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through... -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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...Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. PLoS ONE 13(2): e0192858. https://doi.org/10.1371/journal.pone.0192858
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Protein Microarray Analyser
Protein microarray data processing and normalization
The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. -
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MSqBAT
Label-free protein quantification for LC-MS
...Christoph Rösli at the Heidelberg Institude for Stem Cells and Experimental Medicine (HI-STEM) and the German Cancer Research Center (DKFZ). It’s main features are 1) Label-free, MS1-based quantification 2) Support both LC-MALDI-MS- as well as LC-ESI-MS data 3) Supports both GeLC-MALDI-MS- and GeLC-ESI-MS data 4) Convenient, graphical user interface Acknowledgements The development of MSqBAT is kindly supported by YourKit Java Profiler. -
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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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VirtualDNA
Make your own flowers
virtualDNA is a Processing3 game with an Android APK file in it. You can make your own flowers by crossing a flowerpool. There is a gamelike feature where you have to make a flower that ressembles a given one. -
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Lab Inventory
Rediscover the Simplicity www.atgclabs.com
Request new Lab Inventory feature or module and receive a free Single User version with new feature. Help us to improve Lab Inventory. We want to hear your feedback! https://www.atgclabs.com/products/li The Lab Inventory System is an innovative, easy to learn solution for research laboratories. You can quickly and easily upload your existing Excel based inventory and get started in minutes, manage laboratory inventory, place orders and keep track of them in one place. Lab Inventory... -
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Science & Engineering Inventory
Rediscover the Simplicity http://www.atgclabs.com/
Request new Lab Inventory feature or module and receive a free Single User version with new feature. Help us to improve Lab Inventory. We want to hear your feedback! https://www.atgclabs.com/products/li The Lab Inventory System is an innovative, easy to learn full-featured solution for research laboratories. You can quickly and easily upload your existing Excel based inventory and get started in minutes, manage laboratory inventory, place orders and keep track of them in one... -
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owl reasoning over big biomedical data
A OWL reasoning framework for the analysis of big biomedical data
A general OWL reasoning framework for the analysis of big biomedical data and implement a MapReduce-based property chain reasoning prototype system. OWL reasoning method is ideally suitable for problems involved complex semantic associations because it is able to infer logical consequences based on a set of asserted rules or axioms. MapReduce framework isused to solve the problem of scalability. In our experiment, we focus on the discovery of associations between Traditional Chinese Medicine... -
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Lab Storage
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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Sample Tracking
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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Phanto_maJ
build three dimensional structure
...PhantomaJ is thus "ready to use" for most users, but advanced users can choose to modify specific parameters such as intersection mode, intensity decrease function or virtual real three dimension. In addition, adding a new "basic form" consiste for advanced users to write two short java file ( one describing the new form geometry and the other transcripting this geometry in java3D world ). PhantomaJ is the indispensable tool for who want to create phantom bank of simply an unique complexe structure very easily. -
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Sequencia
Protein Primary Sequnece Analysis
...This work includes all the Physiochemical Properties- related to Primary Sequence Analysis under a common platform. JAVA, BIOJAVA were used under Platform Independent architecture. The Tool includes Properties of being offline where result can be stored in Text Format, here we can paste more than one sequence and also upload FASTA file to compute Parameters. -
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available... -
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Drug Extraction
Drug name extraction
Drug name recognition and normalisation/grounding to DrugBank ids and standard names. Package provides 2 taggers: 1. DrugTagger - CRF-based with DrugBank presence feature (see feature set for details). 2. DrugnameGazetteer - gazetteer/dictionary-based. Dictionary created from DrugBank.ca database. Both taggers include grounding/normalisation to DrugBank ids and standard names. Feature set: Word, Word-1, Word+1, Word-1_Word, Word_Word+1, DrugBankPresence, POS DrugBankPresence...
