The European Molecular Biology Open Software Suite

1
http//www.hgmp.mrc.ac.uk/Software/EMBOSS/
The European Molecular Biology Open Software
Suite
Jon Ison Proteomics Applications Group MRC HGMP
Resource Centre, UK
2
http//www.hgmp.mrc.ac.uk/Software/EMBOSS/

• Over 200 applications

• Sequence analysis (alignment, profiles, motifs
  etc)

• Other stuff (feature tables, graphical output,
  database indexing more !)

• Automatic recognition of variety of 42 sequence
  formats

• Standard report formats are used for output.

• New additions for proteomics protein structure
  (pdb, scop and cath)

• Applications can be run entirely from the
  command line

• Easy to imbed applications in scripts or
  automate GUI development

• Many GUI's for emboss are now available

• Jemboss is our own and is guaranteed to be
  upward compatible

Applications and Interfaces
3
http//www.hgmp.mrc.ac.uk/Software/EMBOSS/

• Over 250,000 lines of code (half of which is
  library code)

• AJAX is the core library for data structures and
  low-level algorithms

• Easy memory management (dynamic strings, arrays
  etc)

• NUCLEUS library is specific to sequence analysis
  (alignment etc)

• New additions for CORBA / Grid.

• New additions for high-level graphics library

• EMBOSS is Open Source

• Applications are under General Public License
  (GPL)

• Libraries are under Library GPL

• Maximum flexibility / encourages development

• EMBOSS is free

Libraries and Licenses
4
http//www.hgmp.mrc.ac.uk/Software/EMBOSS/
Alan Bleasby Peter Rice Gary Williams Tim
Carver Jon Ison Lisa Mullan Hugh Morgan Waqas
Awan Ranjeeva Ranasinghe Claude Beazley David
Martin Val Curwen James Bonfield Thomas
Laurent Rodrigo Lopez Thon de Boer Mark
Faller Others (sorry )

• Maintained by loose collection of interested
  people

• Very active development

• Access to repository is restricted

• but please join in !

• New additions for high-level graphics library

• Nightly compilation checks

• Quality assurance via test data sets

• Mailing lists and regular training courses

Maintenance and Support