BOL: Related items

NCBI to assist in Virus Hunting Data Science Hackathon

BioStar — Thu, 15 Nov 2018 12:55:01 -0600

NCBI Hackathon are pleased to announce the second installment of the SoCal Bioinformatics Hackathon. From January 9-11, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University!

NCBI Hackathon specifically looking for folks who have experience in computational virus hunting or adjacent fields to identify known, taxonomically-definable and novel viruses from a few hundred thousand metagenomic datasets that we’ll put on cloud infrastructure. This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. If this describes you, please apply! The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).

https://ncbiinsights.ncbi.nlm.nih.gov/2018/11/09/ncbi-sdsu-virus-hunting-data-science-hackathon-january-2019/

New Release of RefSeq !

Abhi — Tue, 16 Jul 2024 10:09:21 -0500

Check out RefSeq release 225, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of July 8, 2024, this full release incorporates genomic, transcript, and protein data containing:

448,507,905 records
334,845,613 proteins
63,542,774 RNAs
Sequences from 152,668 organisms

The release is provided in several directories as a complete dataset and also as divided by logical groupings.

Pango Lineage Analysis !

Abhi — Mon, 15 Nov 2021 03:38:29 -0600

The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by researchers to perform analyses on SARS-COV-2 sequence data.

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html

Mobyle: a new full web bioinformatics framework

Jit — Sun, 07 Jan 2018 19:33:45 -0600

Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/25/22/3005/179064

Heatmapper: web-enabled heat mapping for all

Jit — Mon, 01 Oct 2018 08:34:41 -0500

Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. Heatmapper allows users to generate, cluster and visualize:

1) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments; 2) pairwise distance maps;

3) correlation maps;

4) image overlay heat maps;

5) latitude and longitude heat maps and

6) geopolitical (choropleth) heat maps.

Heatmapper offers a number of simple and intuitive customization options for easy adjustments to each heat map’s appearance and plotting parameters. Heatmapper also allows users to interactively explore their numeric data values by hovering their cursor over each heat map, or by using a searchable/sortable data table view.

Ref https://www.ncbi.nlm.nih.gov/pubmed/27190236

Address of the bookmark: http://www2.heatmapper.ca/

BUSCA: an integrative web server to predict subcellular localization of proteins

BioStar — Thu, 07 Feb 2019 14:08:11 -0600

BUSCA (Bologna Unified Subcellular Component Annotator) is a web-server for predicting protein subcellular localization. BUSCA integrates different tools to predict localization-related protein features (DeepSig, TPpred3, PredGPI and ENSEMBLE3.0) as well as tools for discriminating subcellular localization of both globular and membrane proteins (BaCelLo, MemLoci and SChloro).

Address of the bookmark: http://busca.biocomp.unibo.it/

EFS: an ensemble feature selection tool implemented as R-package and web-application

Jit — Tue, 28 Jan 2020 05:12:23 -0600

The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in EFS, which can be used separately or combined in an ensemble.

https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8

Address of the bookmark: http://efs.heiderlab.de/

PPAI: a web server for predicting protein-aptamer interactions

Jit — Fri, 12 Jun 2020 07:26:23 -0500

PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is freely available at http://39.96.85.9/PPAI

Address of the bookmark: http://39.96.85.9/PPAI/

Web Apollo: a web-based genomic annotation editing platform

Jit — Fri, 28 Jul 2017 04:48:17 -0500

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

Address of the bookmark: http://genomearchitect.github.io/

Frontend: Perl Web framework documentation - Andrej Sali Lab

Jit — Mon, 08 Jan 2018 22:32:03 -0600

The frontend is a set of Perl classes that displays the web interface, allowing a user to upload their input files, start a job, display a list of all jobs in the system, and get back job results. The main saliwebfrontend class must be subclassed for each web service. This class is then used to display the web pages using a set of CGI scripts that are set up automatically by the build system.

Address of the bookmark: https://saliweb.readthedocs.io/en/latest/frontend.html