HIVE Pubcast Beta – Pubmed Buzzfeed for Android Mobile Devices

HIVE Pubcast Beta

:: DESCRIPTION

HIVE Pubcast provides users with the most up-to-date PubMed publications at their fingertips within the fields of genomics and proteomics. Users will be able to read abstracts on each new publication that comes out daily, in addition to sharing their favorite articles with friends and colleagues.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

pubcast

:: REQUIREMENTS

  • Android

:: DOWNLOAD

 HIVE Pubcast

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):498-500. doi: 10.1109/TCBB.2016.2542802. Epub 2016 Mar 23.
Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices.
Goldweber S, Theodore J, Torcivia-Rodriguez J, Simonyan V, Mazumder R.

PubCrawler 2.16 – Update Alerting Service for PubMed and GenBank

PubCrawler 2.16

:: DESCRIPTION

PubCrawler is a free “alerting” service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases.  PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests.

::DEVELOPER

Ken Wolfe’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 PubCrawler

:: MORE INFORMATION

PubMed On Tap 2.7.5 – Search PubMed and PubMed Central with your iPhone, iPod Touch, and iPad

PubMed On Tap 2.7.5

:: DESCRIPTION

PubMed On Tap is an application for your iPhone, iPod Touch, and iPad that lets you search PubMed and PubMed Central while on the go.

::DEVELOPER

PubMed OnTap team

:: SCREENSHOTS

PubMedOnTap

:: REQUIREMENTS

  • iPad/iPhone

:: DOWNLOAD

 PubMed On Tap

:: MORE INFORMATION

Annokey – Gene-based Search for Key-terms in NCBI Gene Database and Associated PubMed Abstracts

Annokey

:: DESCRIPTION

Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 Annokey

:: MORE INFORMATION

RANKER – PubMed-based Literature Mining software

RANKER

:: DESCRIPTION

RANKER is a PubMed-based literature mining software for ranking the importance of genes in a given context.

::DEVELOPER

Dr.Zhang’s Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Orthomcl, BLAST (blastall and formatdb), and mcl.

:: DOWNLOAD

 RANKER

:: MORE INFORMATION

Citation

Yang L, Xu L, He L. 2009.
A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction.
Bioinformatics. 25(17):2244-50.

GLAD4U 20111026 – Gene List Automatically Derived For You

GLAD4U 20111026

:: DESCRIPTION

GLAD4U is a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 8:S20. doi: 10.1186/1471-2164-13-S8-S20. Epub 2012 Dec 17.
GLAD4U: deriving and prioritizing gene lists from PubMed literature.
Jourquin J1, Duncan D, Shi Z, Zhang B.

iPubMed 2.2 – Instant PubMed for iPhone / iPad

iPubMed 2.2

:: DESCRIPTION

The goal of the iPubMed Search is to make it easier to search for publications on MEDLINE database.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

iPubMed

:: REQUIREMENTS

  • Web Server / iOS

:: DOWNLOAD

 iPubMed for iPhone , for iPad

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2321-7. doi: 10.1093/bioinformatics/btq414. Epub 2010 Jul 12.
Interactive and fuzzy search: a dynamic way to explore MEDLINE.
Wang J1, Cetindil I, Ji S, Li C, Xie X, Li G, Feng J.

PURE – Pubmed Article Recommendation System based on Content-based Filtering

PURE

:: DESCRIPTION

PURE is a PubMed article recommendation system based on content-based filtering. PURE has a web interface by which users can add and/or delete their preferred articles. Once articles are registered, PURE then performs model-based clustering of the preferred articles and recommends highly-rated articles by prediction using the trained model. PURE updates PubMed articles and reports recommendation by email on daily-base.

::DEVELOPER

Bio-Knowledge Engineering Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows/Linux/MacOsX
  • Perl
  • MySQL
  • PHP
  • APACHE

:: DOWNLOAD

 PURE

:: MORE INFORMATION

Citation:

Genome Inform. 2007;18:267-76.
PURE: a PubMed article recommendation system based on content-based filtering.
Yoneya T, Mamitsuka H.

PuReD-MCL 20111130 – PubMed Document Clustering

PuReD-MCL 20111130

:: DESCRIPTION

PuReD-MCL (PUbmed RElated Document – MCL) is an efficient algorithm for PubMed document clustering (based on the MCL algorithm) using pre-computed document relatedness.

::DEVELOPER

The Bioinformatics Analysis Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PuReD-MCL

:: MORE INFORMATION

Citation:

Bioinformatics. 2008 Sep 1;24(17):1935-41. Epub 2008 Jul 1.
PuReD-MCL: a graph-based PubMed document clustering methodology.
Theodosiou T, Darzentas N, Angelis L, Ouzounis CA.

pubmed2ensembl – Link Publications in PubMed to Genes in Ensembl

pubmed2ensembl

:: DESCRIPTION

pubmed2ensembl is an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species.

::DEVELOPER

the Nenadic group & the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl
  • Java
  • BioMart

:: DOWNLOAD

 pubmed2ensembl

:: MORE INFORMATION

Citation

PLoS One. 2011;6(9):e24716. Epub 2011 Sep 29.
pubmed2ensembl: a resource for mining the biological literature on genes.
Baran J, Gerner M, Haeussler M, Nenadic G, Bergman CM.