ORCA: a comprehensive bioinformatics container environment for education and research

Abstract Summary The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education and research. The ORCA environment on a server is implemented using Docker containers, but without requiring users to interact directly with Docker, suitable for novices who may not yet have familiarity with managing containers. ORCA has been used successfully to provide a private bioinformatics environment to external collaborators at a large genome institute, for teaching an undergraduate class on bioinformatics targeted at biologists, and to provide a ready-to-go bioinformatics suite for a hackathon. Using ORCA eliminates time that would be spent debugging software installation issues, so that time may be better spent on education and research. Availability and implementation The ORCA Docker image is available at https://hub.docker.com/r/bcgsc/orca/. The source code of ORCA is available at https://github.com/bcgsc/orca under the MIT license.

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Using bio.tools to generate and annotate workbench tool descriptions

F1000Research ◽

10.12688/f1000research.12974.1 ◽

2017 ◽

Vol 6 ◽

pp. 2074 ◽

Cited By ~ 5

Author(s):

Kenzo-Hugo Hillion ◽

Ivan Kuzmin ◽

Anton Khodak ◽

Eric Rasche ◽

Michael Crusoe ◽

...

Keyword(s):

Source Code ◽

Workflow Systems ◽

Major Consequence ◽

Bioinformatics Tools ◽

Bioinformatics Software ◽

User Friendly

Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.

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PETAL: a python tool for deep analysis of biological pathways

Bioinformatics ◽

10.1093/bioinformatics/btaa1032 ◽

2020 ◽

Author(s):

Giuseppe Sgroi ◽

Giulia Russo ◽

Francesco Pappalardo

Keyword(s):

Open Source ◽

Signaling Pathways ◽

Open Source Software ◽

Kegg Pathway ◽

Source Code ◽

Therapeutic Targets ◽

Biological Pathways ◽

Long Distance ◽

Bioinformatics Tools ◽

Novel Therapeutic

Abstract Summary Although several bioinformatics tools have been developed to examine signaling pathways, little attention has been given to ever long-distance crosstalk mechanisms. Here, we developed PETAL, a Python tool that automatically explores and detects the most relevant nodes within a KEGG pathway, scanning and performing an in-depth search. PETAL can contribute to discovering novel therapeutic targets or biomarkers that are potentially hidden and not considered in the network under study. Availability PETAL is a freely available open-source software. It runs on all platforms that support Python3. The user manual and source code are accessible from https://github.com/Pex2892/PETAL.

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D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way

10.7287/peerj.preprints.26567v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Floréal Cabanettes ◽

Christophe Klopp

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Web Application ◽

Source Code ◽

Input Sequence ◽

Image Alignment ◽

Large Genome ◽

Open Source Software Package ◽

Large Genomes

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and WEB application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy to install open source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

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D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way

10.7287/peerj.preprints.26567 ◽

2018 ◽

Author(s):

Christophe Klopp ◽

Floréal Cabanettes

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Web Application ◽

Source Code ◽

Input Sequence ◽

Image Alignment ◽

Large Genome ◽

Open Source Software Package ◽

Large Genomes

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D-GENIES: dot plot large genomes in an interactive, efficient and simple way

PeerJ ◽

10.7717/peerj.4958 ◽

2018 ◽

Vol 6 ◽

pp. e4958 ◽

Cited By ~ 89

Author(s):

Floréal Cabanettes ◽

Christophe Klopp

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Web Application ◽

Source Code ◽

Input Sequence ◽

Image Alignment ◽

Large Genome ◽

Open Source Software Package ◽

Large Genomes

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

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Edlib: a C/C++ library for fast, exact sequence alignment using edit distance

10.1101/070649 ◽

2016 ◽

Cited By ~ 2

Author(s):

Martin Šošić ◽

Mile Šikić

Keyword(s):

Exact Sequence ◽

Open Source ◽

Sequence Alignment ◽

Test Data ◽

Edit Distance ◽

Source Code ◽

Memory Usage ◽

Pairwise Sequence Alignment ◽

Link Type ◽

Bioinformatics Tools

AbstractWe present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be a cornerstone for many future bioinformatics tools.Source code, installation instructions and test data are freely available for download at https://github.com/Martinsos/edlib, implemented in C/C++ and supported on Linux, MS Windows, and Mac OS.Contact:[email protected]

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Compressed filesystem for managing large genome collections

Bioinformatics ◽

10.1093/bioinformatics/btz192 ◽

2019 ◽

Vol 35 (20) ◽

pp. 4120-4128

Author(s):

Gonzalo Navarro ◽

Víctor Sepúlveda ◽

Mauricio Marín ◽

Senén González

Keyword(s):

Source Code ◽

Direct Access ◽

Client Server ◽

Large Genome ◽

Compression System ◽

System Calls ◽

Network Time ◽

Order Of Magnitude

Abstract Motivation Genome repositories are growing faster than our storage capacities, challenging our ability to store, transmit, process and analyze them. While genomes are not very compressible individually, those repositories usually contain myriads of genomes or genome reads of the same species, thereby creating opportunities for orders-of-magnitude compression by exploiting inter-genome similarities. A useful compression system, however, cannot be only usable for archival, but it must allow direct access to the sequences, ideally in transparent form so that applications do not need to be rewritten. Results We present a highly compressed filesystem that specializes in storing large collections of genomes and reads. The system obtains orders-of-magnitude compression by using Relative Lempel-Ziv, which exploits the high similarities between genomes of the same species. The filesystem transparently stores the files in compressed form, intervening the system calls of the applications without the need to modify them. A client/server variant of the system stores the compressed files in a server, while the client’s filesystem transparently retrieves and updates the data from the server. The data between client and server are also transferred in compressed form, which saves an order of magnitude network time. Availability and implementation The C++ source code of our implementation is available for download in https://github.com/vsepulve/relz_fs.

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dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes

10.1101/108142 ◽

2017 ◽

Cited By ~ 3

Author(s):

Matthew R. Olm ◽

Christopher T. Brown ◽

Brandon Brooks ◽

Jillian F. Banfield

Keyword(s):

Time Series ◽

Source Code ◽

Computational Time ◽

Average Nucleotide Identity ◽

Microbial Genomes ◽

Large Genome ◽

Link Type ◽

Assembly Method ◽

Inaccurate Estimation ◽

Genome Distance

The number of microbial genomes sequenced each year is expanding rapidly, in part due to genome-resolved metagenomic studies that routinely recover hundreds of draft-quality genomes. Rapid algorithms have been developed to comprehensively compare large genome sets, but they are not accurate with draft-quality genomes. Here we present dRep, a program that sequentially applies a fast, inaccurate estimation of genome distance and a slow but accurate measure of average nucleotide identity to reduce the computational time for pair-wise genome set comparisons by orders of magnitude. We demonstrate its use in a study where we separately assembled each metagenome from time series datasets. Groups of essentially identical genomes were identified with dRep, and the best genome from each set was selected. This resulted in recovery of significantly more and higher-quality genomes compared to the set recovered using the typical co-assembly method. Documentation is available at http://drep.readthedocs.io/en/master/ and source code is available at https://github.com/MrOlm/drep.

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Source code

TCP/IP Essentials ◽

10.1017/cbo9781139167246.016 ◽

2004 ◽

pp. 236-252

Keyword(s):

Source Code

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SISTEM INFORMASI MANAJEMEN PENGARSIPAN BERBASIS FRAMEWORK CODE IGNITER UNTUK MENTERTIBKAN PELAYANAN SURAT MENYURAT

INTERNAL (Information System Journal) ◽

10.32627/internal.v2i1.70 ◽

2019 ◽

Vol 2 (1) ◽

pp. 1-16

Author(s):

Nana Suarna

Keyword(s):

Source Code ◽

Web Based

Seiring waktu, jumlah surat dalam sebuah perusahaan semakin hari makin banyak, sehingga muncul permasalahan dalam mengelolanya administrasi suarat, baik ketika dalam pencatatan surat maupun proses disposisi, serta pada saat pencarian arsip surat. Hampir sebagai besar surat yang ada di kantor-kantor masih disimpan dalam bentuk file-file yang masih bersifat manual, sehingga memungkinkan surat tersebut menunpuk, dan memerlukan waktu yang lama dalam pencarian dan pemrosesannya. Dengan dibangunnya sistem manajemen pengarsipan bertujuan untuk mengatasi permasalahan-permasalahan tersebut di atas. Pemrograman saat ini, baik desktop maupun web based, semakin marak pengerjaannya menggunakan framework code igniter berbasis PHP. Framework CI memang dikembangkan untuk memudahkan dalam developing aplikasi dengan struktur file source code-nya menggunakan pendekatan Models-Views-Controller (MVC) dan pemrograman berorientasi objek, oleh sebab itu penulis menggunakan CI dalam developing aplikasi ini. Aplikasi sistem manajemen surat dan pengarsipan ini dapat diakses dalam internal perusahaan web, yang bertujuan untuk memudahkan karyawan dalam pengelolaan dan mengaksesnya surat menyurat, selain itu aplikasi ini juga memberikan kemudahan dalam proses pencatatan surat, disposisi, dan proses pencarian sehingga aplikasisi ini memiliki performa yang handal, mudah untuk di-maintenance dan dikembangkan lebih lanjut seiring perkembangan kebutuhan penggunanya.

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