BioTools

Useful for biomedical research. Links clicked will open in a new browser window or tab.

 

Basics & Bibliography

  1. Benchwork videos
  2. Book "Human Herpesviruses" (2007)
  3. Current Protocols' Tools & Calculators
  4. ConvertWorld
  5. Formulas that describe solutions
  6. Gantter | GanttProject (Project management)
  7. PubMed (customized search)
  8. SciencePrimer Calculators and Convertion tools
 

Bioinformatics (incl. evolution analysis)

  1. FaBox (fasta sequence toolbox)
  2. Galaxy (web-based platform for data intensive biomedical research)
  3. Java MolBio Tools (JaMBW)
  4. jModeltest
  5. MEGA Software
  6. Mobyle Portal
  7. Molecular Biology Freeware
  8. PhyML
  9. PathGuide (biological pathways listing)
  10. Sequence Manipulation Suite (SMS): Version 1 | Version 2
  11. SYFPEITHI (Epitope prediction)
  12. VectorNTI Tutorial
 

Cell culture & analysis

  1. CellMiner & NCI60 cells panel
  2. Cellosauros (cell lines database)
  3. CCLE (Cancer Cell Line Encyclopedia, Broad Inst.)
  4. Cell types successfully transfected with the Neon® Transfection System
  5. Database of Cross-contaminated or Misidentified Cell Lines (ICLAC)
  6. Extreme Limiting Dilution Analysis (ELDA)
  7. Search STR Database  (ATCC)
  8. Search STR Database (via DSMZ)
 

Documents & Reference

  1. BitesizeBio.com
  2. Cell Signaling Pathways & Tables
  3. Cell Signaling Reference Material
  4. CDC's Biosafety Quick Tutorial
  5. EQUATOR Network (reporting guidelines for health sciences)
  6. Information hyperlinked over Proteins (IHoP)
  7. Selected biosafety docs
 

Forums & discussion groups

  1. ProtocolOnline BioForum
  2. UNESP BioForum
 

Genetic manipulation & clonning

  1. AddGene
  2. NEBioCaculator™
  3. NEB Tools   (Enzyme Finder, Enzyme Cutter, Double Digests, etc.)
  4. Plasmid Guide (AddGene)
 
 

PCR (including primer design tools)

  1. Copy number calculator for qPCR
  2. IDT™ SciTools
  3. NCBI PrimerBlast
  4. RTPrimer Database
  5. Offline Software GeneLink™ Oligo Design Tools and Bio Calculators  
  6. Offline Software GeneLink™ Oligo Explorer Suite
  7. Offline Software OligoExplorer 1.1
 

Protocols & Reagents

  1. Bio-protocol.org
  2. Free featured Cold Spring Harbor  protocols
  3. Labome - Reviews on antibodies and other reagents
  4. Nature ProtocolExchange
  5. Protocol Online
 

Sequence manipulation & analysis

  1. BioEdit Sequence Aligment Editor
  2. JaMBW Reverse, complement, inverse
  3. Eletropherogram Quality Analysis
  4. NCBI BLAST
  5. NCBI NucleotideBlast (nBlast)
  6. Offline Software Chromas
  7. Offline Software GeneRunner
 

Scienciometry

  1. Science metrics (via Harzing's PoP)
  2. Scimago Journal & Country Rank

Offline Software Software to be downloaded and used offline