<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34912?offset=190 https://bioinformaticsonline.com/bookmarks/view/43943/bioinformatics-tutorial Mon, 22 Aug 2022 23:56:22 -0500 https://bioinformaticsonline.com/bookmarks/view/43943/bioinformatics-tutorial <![CDATA[Bioinformatics Tutorial !]]> This site aims to be a useful resource for bioinformatics beginners. Feel free to jump right in with the section most relevant to you, and if you're not sure, then the place to start is definitely Unix

Address of the bookmark: https://astrobiomike.github.io/

]]> Neel https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist Fri, 02 Mar 2018 06:54:15 -0600 https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist <![CDATA[Python learning resources for bioinformatics and computational biologist !]]> Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries.

Professionally, Python is great for backend web development, data analysis, artificial intelligence, and scientific computing. Many developers have also used Python to build productivity tools, games, and desktop apps, so there are plenty of resources to help you learn how to do those as well.

For pros and cons visit http://www.bestprogramminglanguagefor.me/why-learn-python and http://bioinformaticsonline.com/discussion/view/459/python-vs-perl

More resources at https://github.com/CodementorIO/Python-Learning-Resources

Following are the list of useful python programming resources:

]]> Jit https://bioinformaticsonline.com/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources Tue, 28 Jun 2022 07:32:05 -0500 https://bioinformaticsonline.com/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources <![CDATA[Finding a mimicry game for teaching on-line and mentioned general resources]]> Mimicry and other resources Mimicry games: Great Heliconius game: http://heliconius.org/evolving_butterflies/ (See also https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014) Other one, a bit less friendly: https://ccl.northwestern.edu/netlogo/models/Mimicry Camouflage practical https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/ (NetLogo also has one: https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage) Peppered moth game: https://askabiologist.asu.edu/peppered-moths-game/play.html General resources The always popular Populus: https://cbs.umn.edu/populus/overview Drift & Gene Flow https://cartwrig.ht/apps/genie/ (Cock van Oosterhout has a great ppt to lead students through this) See also https://cartwrig.ht/apps/redlynx/ https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/ NetLogo: http://ccl.northwestern.edu/netlogo/models/index.cgi Population Genetics: https://www.radford.edu/~rsheehy/Gen_flash/popgen/ Evolution in general https://evolution.berkeley.edu/evolibrary/home.php Mitochondrial Eve: https://projects.ncsu.edu/cals/gn/ex/mit-eve.html Y chromosomes: https://projects.ncsu.edu/cals/gn/ex/y-chrom.html A professional online package from Michael Kasumovic: https://arludo.com/ a compilation of resources: https://planted.botany.org/index.php?P=Home Finally, Donald Forsdyke has some great on-line videos explaining evolutionary principles (occasionally in a fake Scottish accent): http://post.queensu.ca/~forsdyke/videolectures.htm

 

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/35108/mobyle-a-new-full-web-bioinformatics-framework Sun, 07 Jan 2018 19:33:45 -0600 https://bioinformaticsonline.com/bookmarks/view/35108/mobyle-a-new-full-web-bioinformatics-framework <![CDATA[Mobyle: a new full web bioinformatics framework]]> 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

]]> Jit 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/bookmarks/view/38908/busca-an-integrative-web-server-to-predict-subcellular-localization-of-proteins Thu, 07 Feb 2019 14:08:11 -0600 https://bioinformaticsonline.com/bookmarks/view/38908/busca-an-integrative-web-server-to-predict-subcellular-localization-of-proteins <![CDATA[BUSCA: an integrative web server to predict subcellular localization of proteins]]> 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/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40721/efs-an-ensemble-feature-selection-tool-implemented-as-r-package-and-web-application Tue, 28 Jan 2020 05:12:23 -0600 https://bioinformaticsonline.com/bookmarks/view/40721/efs-an-ensemble-feature-selection-tool-implemented-as-r-package-and-web-application <![CDATA[EFS: an ensemble feature selection tool implemented as R-package and web-application]]> 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/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41863/ppai-a-web-server-for-predicting-protein-aptamer-interactions Fri, 12 Jun 2020 07:26:23 -0500 https://bioinformaticsonline.com/bookmarks/view/41863/ppai-a-web-server-for-predicting-protein-aptamer-interactions <![CDATA[PPAI: a web server for predicting protein-aptamer interactions]]> 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/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32948/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology Tue, 23 May 2017 05:28:56 -0500 https://bioinformaticsonline.com/bookmarks/view/32948/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology <![CDATA[SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology]]> SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/35119/frontend-perl-web-framework-documentation-andrej-sali-lab Mon, 08 Jan 2018 22:32:03 -0600 https://bioinformaticsonline.com/bookmarks/view/35119/frontend-perl-web-framework-documentation-andrej-sali-lab <![CDATA[Frontend: Perl Web framework documentation - Andrej Sali Lab]]> 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

]]> Jit