BOL: Related items

Bioinformatics Training Material !

BioStar — Sat, 18 Mar 2023 11:26:18 -0500

Glittr is a curated list of bioinformatics training material.
All material is:

In a GitHub or GitLab repository
Free to use
Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

16sRNA Database Download

LEGE — Wed, 24 Apr 2024 04:33:15 -0500

Downloading 16S rRNA databases can be crucial for various bioinformatics analyses, especially in microbiome research. However, it's important to note that databases can vary based on your specific needs, such as the taxonomic coverage you require or the type of analysis you're performing. Here's a general guideline on how you can obtain 16S rRNA databases:

NCBI (National Center for Biotechnology Information):
- NCBI provides various databases related to genetic information, including 16S rRNA sequences.
- You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
- Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
- You can download sequences individually or in batches using the provided tools.
GreenGenes:
- GreenGenes is a widely used 16S rRNA gene sequence database.
- You can access it at http://greengenes.secondgenome.com/.
- GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.
SILVA:
- SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
- It covers not only 16S rRNA but also other ribosomal RNA sequences.
- SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.
Ribosomal Database Project (RDP):
- RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
- It provides tools for sequence analysis and classification.
- You can download sequences and taxonomy information from their website.
QIIME (Quantitative Insights Into Microbial Ecology):
- QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
- It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
- QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

Queensland Centre for Medical Genomics, Grimmond Lab

Sun, 14 Jul 2013 11:58:34 -0500

Queensland Centre for Medical Genomics

Research Area:
pancreatic cancer; ovarian cancer; prostate cancer; bowel cancer; brain cancer; endometrial cancer; breast cancer; personalised medicine; high-throughput genomics

Link @ http://www.imb.uq.edu.au/sean-grimmond

Complex Systems: From Physics to Biology October 15-16 2013 at JNU Convention Center

Mon, 23 Sep 2013 10:17:17 -0500

The symposium intents to focus on complex systems arising in a variety of settings in physics and biology. In particular, applications of the concepts of physics to biological sciences will be the major theme of this meeting.

Selected Topics:

Cluster Dynamics
Non-equilibrium Statistical Mechanics
Forced Systems
Hamiltonian Dynamics
Synchronization & Control
Genomics & Systems Biology
Computational Neuroscience
Econophysics

More @ http://www.jnu.ac.in/Conference/SCS2013/

Memories Can Be Passed Down Through DNA

Sat, 10 May 2014 21:24:10 -0500

The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well. Read More: Parental olfactory experience influences behavior and neural structure in subsequent generations http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html "Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood." What Is Epigenetics? http://www.sciencemag.org/content/330/6004/611 "The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics." Epigenetics http://en.wikipedia.org/wiki/Epigenetics Watch More: How to Change Your Genes https://www.youtube.com/watch?v=B5DU9lgbsSE TestTube Wild Card http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC Is Sexiness Hereditary? https://www.youtube.com/watch?v=z6STRCncvM8 ____________________ DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. Watch More DNews on TestTube http://testtube.com/dnews Subscribe now! http://www.youtube.com/subscription_center?add_user=dnewschannel DNews on Twitter http://twitter.com/dnews Anthony Carboni on Twitter http://twitter.com/acarboni Laci Green on Twitter http://twitter.com/gogreen18 Trace Dominguez on Twitter http://twitter.com/trace501 DNews on Facebook http://facebook.com/dnews DNews on Google+ http://gplus.to/dnews Discovery News http://discoverynews.com

Rolland-Lagan lab

Sun, 14 Jul 2013 12:57:57 -0500

The Rolland-Lagan lab at the University of Ottawa is specializing in computational and developmental biology. We use a combination of experimental work, microscopy, image analysis and computer simulations to explore developmental mechanisms in two and three dimensions.

Research Area

Developmental biology, Computational biology, Simulation modeling, Image data analysis

Link @ http://mysite.science.uottawa.ca/arolland/index.html

Should you get sequenced? Not all bad genes predict disease

Rahul Agarwal — Thu, 29 Aug 2013 15:10:53 -0500

“What we really don’t know yet is whether the predictive aspects of the genome are going to turn out to be beneficial or potentially harmful”

“As we roll out genomic medicine we are fighting against this society-wide misconception that having the bad gene means you’re going to get the disease. That’s only true in a very few cases.”

Source:Today Health

Address of the bookmark: http://www.today.com/health/should-you-get-sequenced-not-all-bad-genes-predict-disease-8C11017154

A History of Bioinformatics (in the Year 2039)

Wed, 23 Jul 2014 06:37:51 -0500

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

What is Healthcare Informatics?

Wed, 12 Mar 2014 14:49:54 -0500

Incorporating information technologies and information management, this work describes evolving areas of efficiency in the healthcare industry due to healthcare informatics enhancements. Beginning with an overview of how information management can enhance organizational efficiency the book delves into how informatics can impact productivity for healthcare providers and reduce costs. It stresses the incorporation of available information technologies along with appropriate management tactics to ensure the most effective informatics outcomes that can drive efficiencies. Areas that are addressed include project management in healthcare, knowledge management, decision support systems, business intelligence, Six Sigma, and advanced analytics such as data mining.

The Global Alliance for Genomics and Health (GA4GH)

Jit — Sat, 08 Feb 2020 07:37:31 -0600

The Global Alliance for Genomics and Health (GA4GH) is a policy-framing and technical standards-setting organization, seeking to enable responsible genomic data sharing within a human rights framework.

GA4GH core funders and sponsors enable our work and allow us to convene the international genomic data sharing community.

https://www.ga4gh.org/

Address of the bookmark: https://www.ga4gh.org/