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APRICOT

A tool for sequence-based identification and characterization of protein classes

https://pypi.python.org/pypi/bio-apricot

APRICOT is a computational pipeline for the identification of specific functional classes of interest in large protein sets. The pipeline uses efficient sequence-based algorithms and predictive models like signature motifs of protein families for the characterization of user-provided query proteins with specific functional features. The dynamic framework of APRICOT allows the identification of unexplored functional classes of interest in the large protein sets or the entire proteome.

Biology Dictionary

https://biologydictionary.net/

Biology is the study of living things. It is broken down into many fields, reflecting the complexity of life from the atoms and molecules of biochemistry to the interactions of millions of organisms in ecology. This biology dictionary is here to help you learn about all sorts of biology terms, principles, and life forms. Search by individual topic using the alphabetized menu below, or search by field of study using the menu on the left.

Birch

http://home.cc.umanitoba.ca/~psgendb/

  • is a comprehensive desktop bioinformatics system integrating many of the commonly-used bioinformatics programs
  • is a framework of tools, files, and documentation for organizing and managing a bioinformatics core facility
  • can be customized by seamlessly merging 3rd party applications into BIRCH

CellTracker

http://celltracker.website/index.html

CellTracker is an image processing software to perform automated, semi-automated, and manual cell migration detection.

The main goals of the software are:

  • automated image quality enhancement using vignetting and alignment correction;
  • detection and tracking of cells;
  • editing cell paths and statistical analysis of the cell motion.

The major challenge what we addressed is to perform the above goals on phase-contrast and DIC images. Nevertheless, CellTracker works on fluorescent images as well.

The program is written in MatLab with a graphical user interface, it requires MatLab 2012, Image Processing Toolbox 8.1 and for some optional functions Curve Fitting Toolbox 3.3 or later versions. The output statistics are stored in human readable table file (Excel, .csv). Furthermore, it is possible to create movies and visualize migration over time in 3D graphs (x, y, time).

CRImage – tumour image analysis

http://www.markowetzlab.org/software/CRImage.php

CRImage provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images. In particular, it allows cellularity scoring of tumours which can then be applied to correct molecular assay data for varying cellularity. The package also comes with a novel algorithm for copy-number data correction, given SNP microarray data and cellular content of the tumours estimated by the image analysis.

DRNApred

DNA- and RNA-binding residues predictor

http://biomine.cs.vcu.edu/servers/DRNApred/

DRNApred was designed using a new dataset with both DNA-and RNA-binding proteins, regression that penalizes cross-predictions, and a novel two-layered architecture. DRNApred outperforms state-of-the-art predictors of DNA-or RNAbinding residues on a benchmark test dataset by substantially reducing the cross predictions and predicting arguably higher quality false positives that are located nearby the native binding residues.

ImmuneQuest

http://immunequest.com/

ImmuneQuest is an innovative educational game for college students that brings immunology to life. Designed to augment an educator’s existing curriculum, ImmuneQuest allows students to build and control a virtual immune system to defend their human host from increasingly cunning microbes.

ORIO

Online Resource for Integrative Omics

https://orio.niehs.nih.gov/

ORIO (Online Resource for Integrative Omics) is a platform for integration of whole genome data accessible to life scientists with minimal computational expertise. ORIO is implemented in a modern web framework that intuitively organizes data and analysis results. All features are accessible using its web interface; environmental health scientists and other users may upload data, set-up analyses, and view results all through an interactive GUI. ORIO hosts 4,506 human and mouse datasets from the ENCODE research project, providing a point of access for life scientists to contextualize their own data within a rigorously controlled consortial dataset. Statistical tests are also implemented next to dynamic displays of analysis results, allowing transitions from discovery-based to hypothesis-based inquiries. ORIO was consciously designed to make minimal assumptions about data during analysis, allowing its applications to a variety of experiment types and study designs.

RCAS

RNA Centric Annotation System

http://rcas.mdc-berlin.de/

RCAS is an automated system that provides dynamic genome annotations for custom input files that contain transcriptomic regions. Such transcriptomic regions could be, for instance, peak regions detected by CLIP-Seq analysis that detect protein-RNA interactions, RNA modifications (alias the epitranscriptome), CAGE-tag locations, or any other collection of target regions at the level of the transcriptome. RCAS is designed as a reporting tool for the functional analysis of RNA-binding sites detected by high-throughput experiments. It takes as input a BED format file containing the genomic coordinates of the RNA binding sites and a GTF file that contains the genomic annotation features usually provided by publicly available databases such as Ensembl and UCSC. RCAS performs overlap operations between the genomic coordinates of the RNA binding sites and the genomic annotation features and produces in-depth annotation summaries such as the distribution of binding sites with respect to gene features (exons, introns, 5’/3′ UTR regions, exon-intron boundaries, promoter regions, and whole transcripts). Moreover, by detecting the collection of targeted transcripts, RCAS can carry out functional annotation tables for enriched gene sets (annotated by the Molecular Signatures Database) and GO terms. As one of the most important questions that arise during protein-RNA interaction analysis; RCAS has a module for detecting sequence motifs enriched in the targeted regions of the transcriptome. A full interactive report in HTML format can be generated that contains interactive figures and tables that are ready for publication purposes.

ScientiFig

https://grr.gred-clermont.fr/labmirouse/software/index.html

 

ScientiFig is a free tool to help you create, format or reformat scientific figures. ScientiFig creates and maintains the layout of both simple figures consisting of similarly sized images or graphs and complex figures containing panels with a variety of sizes. ScientiFig automatically takes care of the alignment of the text with respect to the images, and it has tools to make annotating and reformatting bitmap images easy. The software optimally positions scale bars and allows image annotation using regions of interest (ROIs), brackets and floating text. Because figures often contain graphs, we also provide a plug-in called FiguR that can be used with the open-source software R to dynamically generate and import vector-based graphs into figures created by ScientiFig.

UGENE

http://ugene.net/

Unipro UGENE is a free cross-platform genome analysis suite. It is distributed under the terms of the GNU General Public License. It works on Windows, Mac OS X or Linux and requires only a few clicks to install.

Creating, editing and annotating nucleic acid and protein sequences

Fast search in a sequence

Multiple sequence alignment: ClustalWClustalOMUSCLEKalignMAFFTT-Coffee

PCR in silico

Search through online databases: NCBI, PDB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, DAS servers

Local and NCBI Genbank BLAST search

Open reading frames finder

Restriction enzyme finder with integrated REBASE restriction enzymes list

Integrated Primer3 package for PCR primer design

Plasmid construction and annotation

Cloning in silico by designing of cloning vectors

Genome mapping short reads with BowtieBWA and UGENE Genome Aligner

Raw NGS data processing

Visualization of next generation sequencing data (BAM files) using UGENE Assembly Browser

Variant calling with SAMtools

RNA-seq data analysis with Tuxedo pipeline (TopHat, Cufflinks, etc.)

ChIP-seq data analysis with Cistrome pipeline (MACS, CEAS, etc.)

SPAdes de novo assembler

HMMER2 and HMMER3 packages integration

Chromatogram viewer

Search for transcription factor binding sites (TFBS) with weight matrix and SITECON algorithms

Search for direct, inverted and tandem repeats in DNA sequences

Local sequence alignment with optimized Smith-Waterman algorithm

Building (using integrated PHYLIP Neighbor JoiningMrBayes or PhyML Maximum Likelyhood) and editing phylogenetic trees

Combining various algorithms into custom workflows with UGENE Workflow Designer

Contigs assembly with CAP3

3D Structure viewer for files in PDB and MMDB formats, anaglyph view support

Protein secondary structure prediction with GOR IV and PSIPRED algorithms

Constructing dotplots for nucleic acid sequences

mRNA alignment with Spidey

Creating and using a shared storage (e.g. for a lab)

Search for a pattern of various algorithms’ results in a nucleic acid sequence with UGENE Query Designer

VisIt

https://wci.llnl.gov/simulation/computer-codes/visit

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (<101 core) desktop-sized projects to large (>105 core) leadership-class computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations. VisIt contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured, adaptive and unstructured meshes. Owing to its customizable plugin design, VisIt is capable of visualizing data from over 120 different scientific data formats