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an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages.
Keywords:
Utilities
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each ...
tools to analyze and comprehend high-throughput genomic data.
Installation Client for the BioGrids software collection.
Keywords:
Utilities
a set of tools for biological computation written in Python by an international team of developers.
Keywords:
Utilities
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
the Amazon Web Services (AWS) SDK for Python, which allows Python developers to write software that makes use of Amazon services like S3 and EC2. Boto provides an easy to use, object-oriented API as well as low-level direct service access.
a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.
designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
a Workflow Management System geared towards scientific workflows.
redistributable software libraries to support CUDA applications for Linux.
Keywords:
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself. cython is installed as a module within python.
Keywords:
Python Module
GNU datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files.
a comprehensive DNASTAR software package that includes the software suites for genomics, structural biology, and molecular biology research.
Limited license: supported at Boston Children's Hospital
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
a powerful and comprehensive suite of molecular biology and NGS analysis tools.
Limited license: supported at Boston Children's Hospital
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
Keywords:
Utilities
a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language. The goal is to handle phylogenetic trees in Newick, Nexus and PhyloXML formats, through several basic commands. Each command may print result (a tree for example) in the standard output, and thus can be piped to the standard input of the next gotree command.
Installation client for Harvard Medical School
Limited license: supported at Harvard Medical School
a statistical software package offered by IBM that is used for statistical analysis. Includes IBM SPSS Modeler, IBM SPSS Statistics, IBM SPSS Analytic Server, & IBM SPSS Collaboration & Deployment Services.
Limited license: supported at Boston Children's Hospital
a language-agnostic HTML notebook application for Project Jupyter.
Keywords:
Pipelines
the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.
Keywords:
Utilities
a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano. Developed with a focus on enabling fast experimentation, Keras is a deep learning library that allows for easy and fast prototyping (through user friendliness, modularity, and extensibility); supports both convolutional networks and recurrent networks, as well as combinations of the two; and runs seamlessly on ...
a system designed for automated collection of images from a transmission electron microscope; it includes the python-side programs written in python and c, the MySQL database and server, and the mainly php-based image and data viewers on a web server.
Keywords:
Bioimaging
a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions.
Limited license: supported at Boston Children's Hospital
Keywords:
Nucleic Acids
a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
a matrix-based, high-performance language for scientific and engineering computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation.
Limited license: supported at Boston Children's Hospital

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Keywords:
Other Tools
an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
Keywords:
Python Module
(Multiple EM for Motif Elicitation) a collection of motif-based sequence analysis tools for discovering motifs in a group of related DNA or protein sequences.
(Mixture-of-Isoforms) for isoform quantitation using RNA-Seq is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. MISO is installed as a standalone program and as a module within python.
an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
Keywords:
a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
Keywords:
Utilities
a reactive workflow framework and programming DSL that ease writing computational pipelines with complex data. It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations. Nextflow extends this approach, adding the ability to define complex program interactions and a ...
contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. NumPy is installed as a module within Python.
Keywords:
Python Module
(Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).
Keywords:
an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.
a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language. pandas is installed as a module within python.
Pediatric Scholar installation client for Boston Children's Hospital
Limited license: supported at Boston Children's Hospital
Keywords:
Utilities
(Pathologically Eclectic Rubbish Lister or sometimes called the Practical Extraction and Reporting Language) a highly capable, feature-rich family of programming languages.
Keywords:
Utilities
predicts the regulatory role of CRP transcription factor in Escherichia coli. PredCRP provides an accurate method for deriving an optimised model (named PredCRP-model) and a set of four interpretable rules (named PredCRP-ruleset) for predicting and analysing the regulatory roles of CRP from sequences of CRP-binding sites.
GraphPad Prism combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization.
an interface to the REDCap Application Programming Interface (API), PyCap is designed to be a minimal interface exposing all required and optional API parameters.
Keywords:
Utilities
a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.
Keywords:
Utilities
an open source deep learning platform that provides a seamless path from research prototyping to production deployment.
cross platform time zone library that brings the Olson tz database into Python and allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo).
Keywords:
Bioimaging
a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.
Keywords:
a free software environment for statistical computing and graphics.
Keywords:
Utilities
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
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a DNA sequence assembly and analysis software package for Sanger Sequencing and Next Generation Sequencing.
Limited license: supported at Boston Children's Hospital
A method and tool to control single-cell RNA-seq data quality.
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
Data Analysis and Statistical Software
Limited license: supported at Boston Children's Hospital
(Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.
cleans up raw data files and converts them to pdf format with LaTex. TeX Live offers an easy way to get up and running with the TeX document production system.
Keywords:
Utilities
(Visualization Tool Kit)f a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
a blending of the wxWidgets C++ class library with the Python programming language.
an extensible parallel framework, written in Python using OpenMPI libraries that allows researchers to quickly build high throughput big data pipelines without extensive knowledge of parallel programming.
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