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Bioinformatics.org
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Online databases
Online analysis tools
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Latest announcements
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EXCERPT
The OneZoom explorer – available at https://onezoom.org – maps the connections between 2.2 million living species, the closest thing yet to a single view of all species known to science.
The interactive tree of life allows users to zoom in to any species and explore its relationships with others, in a seamless visualisation on a single web page. The explorer also includes images of over 85,000 species, plus, where known, their vulnerability to extinction.
Source: https://www.imperial.ac.uk/news/232634/visually-stunning-tree-known-life-unveiled/
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We are pleased to share our list of computational resources in health care. It covers a wide range of informatics-based fields like chemoinformatics, medical informatics, pharmacoinformatics and bioinformatics. The paper and server are available from the following links.
Paper link: https://doi.org/10.1002/widm.1437
Web server: https://webs.iiitd.edu.in
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March 17-18, 2022
Grand Hotel Mediterraneo
Florence, Italy, and online
http://conference.pixel-online.net/NPSE/callforpapers.php
11th Edition – Hybrid Event
The Conference brings together teachers, researchers, practitioners and project managers from all over the world to share findings, expertise and experience about innovative science teaching and learning methodologies, through on-site and on-line presentations, and social events.
We will deliver a full 2 days programme of inspiring sessions in the framework of a highly interactive hybrid conference experience. We will provide enhanced contents that will give participants greater access to learning, sharing and networking.
- All accepted papers at the conference will be presented on-site and on-line.
- Interactive questions and answers sessions will follow each paper presentation.
- On-site and on-line poster presentation sessions will also be held.
- Networking opportunities will be organized.
All accepted papers will be included in the Conference Proceedings published with ISBN, ISSN and DOI codes.
The publication will be sent to be reviewed for inclusion in the Conference Proceedings Citation Index by Thomson Reuters (ISI-Clarivate). The publication will also be included in Academia and indexed in Google Scholar.
IMPORTANT DATES
Extended abstract submission deadline: November 17, 2021
Notification of abstract evaluation: December 1, 2021
Deadline for paper submission: January 21, 2022
Conference days: March 17-18, 2022
There will be five presentation modalities: oral and poster presentation on-site; oral, poster and asynchronous presentation on-line.
FOR MORE INFORMATION
Contact: science[at]pixel-online.net
Health and Safety issues in relation to COVID-19:
In case participants are not able to attend on-site, online, interactive, attendance/presentation opportunities are available. Participants attending/presenting online will benefit of a discounted fee. Every precaution possible is taken to create a safe environment for participants attending on-site (masks, gloves, distance seating, disinfection etc.). Finally, should the conditions do not allow the conference to be held on-site as expected, the event will shift to a fully virtual format.
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Proteome-pI 2.0 (http://www.isoelectricpointdb2.org) is an updated version of an online database containing information about predicted isoelectric points.
The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography-mass spectrometry, and X-ray protein crystallography.
The following changes have been introduced:
- The number of proteomes included has been increased four-fold (from 5,029 to 20,115)
- New algorithms for isoelectric point prediction have been added (21 algorithms in total)
- The prediction of pKa dissociation constants for over 61 million proteins have been included (5.38 Billion predictions in total)
- The prediction of isoelectric point for in silico digests of proteomes with the five most commonly used proteases (trypsin, chymotrypsin, trypsin+LysC, LysN, ArgC) have been added (9.58 Billion peptides)
The database allows the retrieval of virtual 2D-PAGE plots and the development of customized fractions of proteome based on isoelectric point and molecular weight.
Moreover, Proteome-pI 2.0 facilitates statistical comparisons of the various prediction methods as well as biological investigation of protein isoelectric point space in all kingdoms of life (updated statistics available at http://www.isoelectricpointdb2.org/statistics.html). The database includes various statistics and tools for interactive browsing, searching, and sorting. It can be searched and browsed by organism name, average isoelectric point, molecular weight, or amino acid frequencies. Proteins with extreme pI values are also available. For individual proteomes, users can retrieve proteins of interest given the method, isoelectric point, and molecular weight ranges (this particular feature can be highly useful to limit potential targets in the analysis of 2DPAGE gels or before conducting mass spectrometry).
Finally, some general statistics (total number of proteins, amino acids, average sequence length, amino acid, and di-amino acid frequencies) and datasets corresponding to major protein databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr) database have also been precalculated (see http://www.isoelectricpointdb2.org/download.html).
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ABSTRACT EXCERPT
The knowledge of the history of a subject stimulates understanding. As we study how other people have made scientific breakthroughs, we develop the breadth of imagination that would inspire us to make new discoveries of our own. This perspective certainly applies to the teaching of genetics as hallmarked by the pea experiments of Mendel. Common questions students have in reading Mendel's paper for the first time is how it compares to other botanical, agricultural, and biological texts from the early and mid-nineteenth centuries; and, more precisely, how Mendel's approach to, and terminology for debating, topics of heredity compare to those of his contemporaries?
Article: https://doi.org/10.1186/s13062-021-00308-4
Citation: Poczai, P., Santiago-Blay, J.A. Principles and biological concepts of heredity before Mendel. Biol Direct 16, 19 (2021).
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Bioinformatics is a diverse and exciting field. Best described as data science for the life sciences, it uses computational approaches to extract meaningful information from complex data sets, providing novel insights in biological, clinical and environmental science. This rapidly-growing area of science is driving new discoveries for today's data-driven health and life science industries.
To meet the growing demand for such expertise, the University of Birmingham has launched an innovative new programme – the Online MSc Bioinformatics (https://landing.birmingham.ac.uk/uob/msc-bio?utm_source=Bioinformatics&utm_medium=Article&utm_campaign=Article_Bioinformatics_BIO_Sept21).
Designed to bridge expertise in both data and life sciences in order to enable the best tools to analyse the best data, the programme is delivered 100% online. Combining different fields of study, including computer sciences, molecular biology, biotechnology, statistics, machine learning and engineering, it seeks to appeal to biologists and healthcare professionals interested in data analysis, as well as statisticians, computer or data scientists wishing to apply their skills in biology.
Expertly adapted for online audiences from the campus-based programme, which is ranked top-20 in the UK for both Biology and Computer Science by QS 2021, the curriculum is delivered by the Centre for Computational Biology – a cross-campus initiative providing broad expertise in data science for the life sciences through both research and training – the programme is uniquely placed to support those eager to get ahead in this invaluable industry.
Led by industry renowned Professor of Bioinformatics, Prof Jean-Baptiste Cazier – founder and designer of both the Centre for Computational Biology and the campus Bioinformatics MSc – students will learn to communicate effectively with fellow biologists, computer scientists and statisticians, interact with complex data sets, learn and teach with data and improve their coding skills.
Applications are now open for the February 2022 intake – request more information (https://landing.birmingham.ac.uk/uob/msc-bio?utm_source=Bioinformatics&utm_medium=Article&utm_campaign=Article_Bioinformatics_BIO_Sept21) to find out how to apply today.
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October 16-19, 2021
Indraprastha Institute of Information Technology (IIIT-D)
Delhi, India
https://webs.iiitd.edu.in/hitsummit/
Department of Computational Biology at Indraprastha Institute of Information Technology (IIIT-D), Delhi in association with APBians is organizing a "Health Informatics Summit" from 16-19 October 2021. No registration fees required. For more information, please visit the website.
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A new version of FirstGlance in Jmol http://FirstGlance.Jmol.Org (free and open source as always) provides guided visual exploration of macromolecular structures with remarkable ease of use (no command language needed). The "FirstGlance" it offers is maximally informative.
This new version should help to de-mystify electron density maps by making them super easy to look at – both for X-ray, and for Electron Microscopic Coulombic density maps. You simply "Find" a few residues (click "Find.." in the Focus Box and, for example, with 1ijw enter Ser174,DA10) which identifies them with yellow halos, whereupon the density map is just one more click. See slides 5-6 showing FirstGlance-generated animations of density maps at http://tinyurl.com/movingmolecules.
For educators and students, this new version starts up in a simplified mode, with fewer details cluttering the Molecule Information Tab and hiding advanced tools in the Tools tab. Still, much is offered about the model, including reliability (Rfree interpreted for you), number of chains and which are sequence-identical, sequences, missing residues, full names of ligands, and the biological assembly. The Views Tab shows secondary structure, hydrophobic cores, charge distribution, etc. The Tools Tab shows protein crosslinks, ends of chains, salt bridges, cation-pi interactions, and non-covalent interactions with any moiety you specify.
Click "Show More Details" only if you want detailed analyses of alternate locations (which can be animated) and occupancies, counts of incomplete sidechains, various protein crosslinks, related PDB entries, one-click access to view the PDB data file contents, coloring by temperature/B factor, etc.
This version automatically detects likely cases of the following covalent protein crosslinks (in addition to disulfide bonds, already in FirstGlance for years): isopeptide crosslinks, thioester crosslinks, thioether crosslinks, ester crosslinks, His-Tyr crosslinks, and Lys-Cys NOS crosslinks (first reported a few months ago). Clicking on one crosslink zooms in and shows it in detail, with the electron density map being one further click. Thanks to Amr A. Alhossary for finding some of the examples.
Feedback always welcome!
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Genozip is a universal compressor for genomic files – it is optimized to compress FASTQ, SAM/BAM/CRAM, VCF/BCF, FASTA, GVF, PHYLIP, Chain, Kraken and 23andMe files, but it can also compress any other file (including non-genomic files).
Typically, a 2X-5X improvement over the existing compression is achieved when compressing already-compressed files like .fastq.gz .bam vcf.gz, and up to 200X for a high-sample-count VCF file.
Yes, Genozip can compress already-compressed files (.gz .bz2 .xz .bam .cram).
The compression is lossless – the decompressed file is 100% identical to the original file.
Details: https://genozip.com. Available on conda (conda-forge channel) and https://github.com/divonlan/genozip
Reference:
Lan, D., et al. (2021) Genozip: a universal extensible genomic data compressor Bioinformatics, btab102, https://doi.org/10.1093/bioinformatics/btab102
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| Acknowledgments |
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We wish to thank the following for their support:
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