<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/33976?offset=620 https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics Wed, 20 Aug 2014 22:09:21 -0500 https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics <![CDATA[Pimp your brain: Bioinformatics]]> Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de]]> https://bioinformaticsonline.com/bookmarks/view/37800/heatmapper-web-enabled-heat-mapping-for-all Mon, 01 Oct 2018 08:34:41 -0500 https://bioinformaticsonline.com/bookmarks/view/37800/heatmapper-web-enabled-heat-mapping-for-all <![CDATA[Heatmapper: web-enabled heat mapping for all]]> 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/

]]> Jit https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example Tue, 06 Aug 2024 23:51:51 -0500 https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example <![CDATA[Learn python with example]]>

There are over 21 unique Python project walkthroughs in this content that range from beginner to advanced. See below for the timestamps for these projects:

00:00:00 | How To Navigate These Projects
---
00:01:46 | #1 - Quiz Game (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/quiz_game.py 
---
00:22:00 | #2 - Number Guessing Game (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/number_guesser.py 
---
00:39:49 | #3 - Rock, Paper, Scissors (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/rock_paper_scissors.py 
---
00:54:40 | #4 - Choose Your Own Adventure Game (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/choose_your_own_adventure.py 
---
01:06:47 | #5 - Password Manager (Medium)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/ 
Fernet Cryptography Documentation: https://cryptography.io/en/latest/fernet/ 
---
01:37:37 | #6 - PIG (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project1.py 
---
01:59:07 | #7 - Madlibs Generator (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project2.py 
---
02:15:04 | #8 - Timed Math Challenge (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project3.py 
---
02:28:02 | #9 - Slot Machine (Medium)
Code: https://github.com/techwithtim/Python-Slot-Machine 
---
03:20:43 | #10 - Turtle Racing (Medium)
Code: https://github.com/techwithtim/Turtle-Racing-V2 
Turtle Docs: https://docs.python.org/3/library/turtle.html 
---
04:13:09 | #11 - WPM Typing Test (Medium)
Code: https://github.com/techwithtim/WPM_Typing_Test 
Curses Docs: https://docs.python.org/3/howto/curses.html 
05:09:43 | #12 - Alarm Clock (Easy)
Python Project Idea Blog: https://hackr.io/blog/python-projects 
Sound Effects: https://www.fesliyanstudios.com/royalty-free-sound-effects-download/alarm-203 
---
05:22:07 | #13 - Password Generator (Easy)
Python Project Idea Blog: https://hackr.io/blog/python-projects 
---
05:39:16 | #14 - Shortest Path Finder (Advanced)
Code: https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/path-finder.py 
---
06:14:53 | #15 - NBA Stats & Current Scores (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/nba-scores.py 
---
06:38:22 | #16 - Currency Converter (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/currency-converter.py 
API: https://free.currencyconverterapi.com/
---
06:58:51 | #17 - YouTube Video Downloader (Medium)
Code:  https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/youtube.py 
---
07:09:50 | #18 - Automated File Backup (Medium)
Code: https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/backup.py 
---
07:21:18 | #19 - Mastermind/4 Color Match (Advanced)
---
07:48:20 | #20 - Aim Trainer (Advanced)
Code: https://github.com/techwithtim/Python-Aim-Trainer 
---
08:39:20 | #21 - Advanced Python Scripting (Advanced)
Code: https://github.com/techwithtim/Python-Scripting-Project 

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/4099/sequencing-solutions-to-world-health Thu, 29 Aug 2013 15:05:35 -0500 https://bioinformaticsonline.com/bookmarks/view/4099/sequencing-solutions-to-world-health <![CDATA[Sequencing Solutions to World Health]]> "New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine."

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

]]> Rahul Agarwal https://bioinformaticsonline.com/pages/view/2518/genome-browsers Fri, 16 Aug 2013 19:04:47 -0500 https://bioinformaticsonline.com/pages/view/2518/genome-browsers <![CDATA[Genome Browsers]]> Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/4208/latest-paper-on-comparison-of-mapping-tools Tue, 03 Sep 2013 18:00:38 -0500 https://bioinformaticsonline.com/bookmarks/view/4208/latest-paper-on-comparison-of-mapping-tools <![CDATA[Latest paper on comparison of mapping tools]]> A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013.

http://bmi.osu.edu/hpc/software/benchmark/

http://bmi.osu.edu/hpc/software/pmap/pmap.html

Other similiar papers:

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022

http://bioinformatics.oxfordjournals.org/content/28/24/3169

Some new Mapping tool links:

GSNAP

http://research-pub.gene.com/gmap/

RMAP

http://rulai.cshl.edu/rmap/

mrsFAST

http://mrsfast.sourceforge.net/Home

http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/

BFAST

http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page

SHRiMP (for AB SOLiD color-space reads)

http://compbio.cs.toronto.edu/shrimp/

RazerA 3

http://www.seqan.de/projects/razers/

Address of the bookmark: http://www.biomedcentral.com/1471-2105/14/184

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/9400/largest-genome-sequenced Fri, 21 Mar 2014 13:57:19 -0500 https://bioinformaticsonline.com/bookmarks/view/9400/largest-genome-sequenced <![CDATA[Largest Genome Sequenced]]> The enormous size of the loblolly pine genome having 22 billion base pairs compared to only 3 billion in the human genome. In other words, it is seven times larger than a human’s and also the largest and the most complete conifer genome ever sequenced.

Related Paper:

http://genomebiology.com/2014/15/3/R59/abstract

 

Address of the bookmark: http://www.news.ucdavis.edu/search/news_detail.lasso?id=10859

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool Fri, 25 Apr 2014 10:59:04 -0500 https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool <![CDATA[New RNA Seq tool]]> "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy."

Tool link:

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Address of the bookmark: http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/

]]> Rahul Agarwal https://bioinformaticsonline.com/news/view/10966/genxpro-gmbh Thu, 22 May 2014 07:18:35 -0500 https://bioinformaticsonline.com/news/view/10966/genxpro-gmbh <![CDATA[GenXPro GmbH]]> GenXPro GMbH is service provider for entire spectrum of nucleotide-based information of any biological sample. By combining intelligent data reduction techniques and latest next generation sequencing technologies, our service portfolio provides most accurate and cost efficient solutions for transcriptomic-, genomic- or epigenomic research.

GENXPRO GMBH, ALTENHÖFERALLEE 3, 60438 FRANKFURT MAIN, GERMANY

Website: http://www.genxpro.info/products_and_services/

PHONE: +49 (0)69- 95 73 97 10, FAX: +49 (0)69- 95 73 97 06

EMAIL: info@genxpro.de

]]> Rahul Agarwal https://bioinformaticsonline.com/file/view/13415/genomics-and-sequencing-approach-for-identification-of-biomarkers-to-assess-the-efficacy-of-tgf-%CE%B2ri-inhibitors-of-liver-cancer-in-vivo Tue, 05 Aug 2014 13:55:32 -0500 https://bioinformaticsonline.com/file/view/13415/genomics-and-sequencing-approach-for-identification-of-biomarkers-to-assess-the-efficacy-of-tgf-%CE%B2ri-inhibitors-of-liver-cancer-in-vivo <![CDATA[Genomics and sequencing approach for identification of biomarkers to assess the efficacy of TGF-βRI inhibitors (of liver cancer) in vivo]]> Liver cancer is third leading cause of deaths and fourth most frequent occuring cancer worldwide. There are multiple signaling pathways responsible for causing cancer amongst which TGFb is most important cytokine whose signaling pathway promote cancer. However, main problem is to cure this cancer at late stage where we still have no treatment strategy to tackle this deadly cancer.  Hence we need to find out new therapeutic target. One way is to look the relationships between mRNA, methylation and miRNA data of patients with different pathological conditions (cancer vs control either with inhibitor/not). MiRNA is small RNA molecules known to inhibit mRNA expression of particular gene by binding improperly to 3'UTR region of a gene and hence block binding of TF /translation of gene. CpG regions is known to located at promoter region of gene (5' UTR) and usually hypomethylated which allow to gene to transcribe and translate however sometime this region become hyper-methylated thats prevent expression of host gene. Thus , integration of these three data reveal new targets and pathways important for causing or preventing cancer and also reveal biomarker thats check the effects of inhibitor on signaling pathway underlying liver cancer.

]]> Rahul Agarwal