1. Introducing EMBOSS/ Jemboss European Molecular Biology Open Software Suite Dr. Erik Bongcam-Rudloff

2. History In the beginning was EGCG 1988 - EGCG is started to provide extensions to the GCG package. EGCG is used by up to 10,000 users at 150 centers as an addition to the GCG package. EGCG sought to support the needs of major sequencing initiatives such as the human genome project. Late 1990's - GCG/EGCG is the de facto standard sequence analysis package worldwide. Oxford Molecular (then commercial owners of GCG) close access to the program code preventing further development of EGCG past version 8.1

3. The Birth of EMBOSS Spurred by the continuing demand for new sequence analysis programs the EMBOSS project is started. Core development is funded by the UK research councils and the Welcome Trust as part of their commitment to the Human Genome Project The experience of the EGCG team is used to write an entirely new package from the ground up. EMBOSS has been designed from scratch by scientists for scientists, so it can readily be integrated with the web or other packages. EMBOSS has been licensed as 'Open Source' to ensure continued access to the program code. This prevents anyone from taking your programs away.

4. EMBOSS today Core libraries of routines for sequence manipulation, database access, and so on are available. These libraries are prewritten functions that any programmer can use. They cover simple things like extracting subsequences to complex things like sequence alignments and comparisons. These make writing new programs much easier. More than 80 programs have been written, replacing greater than 90% of the functionality of GCG and adding many functions you will find in no other package. Programs are being contributed at an impressive rate from all over the world and EMBOSS is installed in many laboratories worldwide. Open source means that you have permission to modify and customise the programs to do what you need, without constraint.

5. EMBOSS present and future EMBOSS under development Training courses and documentation These are being actively developed by users and EMBnet. Graphical/Web interfaces. Now the initial EMBOSS release is stable, graphical interfaces are being developed Web-based:W2H, Pise and others Java:JEMBOSS Your own programs Writing an EMBOSS application is quick and easy for a C programmer.

6. Comparing EMBOSS and GCG Some examples: DISTANCES -PHYLIP package EXTRACTPEPTIDE -transeq MAP -Restrict Remap MOTIFS -Patmamotifs PEPDATA -getorf

7. Using EMBOSS All EMBOSS programs can be run from the command line. There is no need to specifically initialise EMBOSS. You can specify everything with options or have EMBOSS prompt you for the inputs to the program By default EMBOSS programs will not ask you lots of questions, just the minimum needed to run the program. If you put the ' -opt ' option on the command line then EMBOSS will ask you for more detailed options. You can get help on any program with the ' -help ' option on the command line. This will list all the inputs a program needs in order to run.

8. Writing EMBOSS programs Fully GPL No purchase necessary EMBOSS Instant bioinformatics! Just add science and 'make'! 1. Write the ACD file to describe the input to your program. Three steps to a new program: 2. Write the program code to initialise your program in EMBOSS using the templates provided. Retrieve the parameters. You can test that you have your program described correctly with the command ' acdc ' int param1; void main(int argc, char * argv) { embInit("program",argc, argv); param1 = ajAcdGetInt("param1");... 3. Now just add the science. Write the code to do the manipulations you need. EMBOSS has many common bioinformatic functions in the AJAX and NUCLEUS libraries.

9. EMBOSS INTERFACES

10. Interfaces Web EMBOSS- W2H PISE EMBOSSS-GUI X-Windows STADEN- SPIN, (+ others coming) Ssh/xterm/Character-based emnu

11. Web interface details Many are being developed: W2H (http://www.hgmp.mrc.ac.uk/Registered/Webapp/e mboss-w2h/) Pise details (http://www- alt.pasteur.fr/~letondal/Pise/) wEMBOSS (http://liv.bmc.uu.se/EMBOSS)

12. Web interface details

13. X-Windows interfaces At least three are being developed: Spin (Staden package) Kaptain (http://userpage.fu- berlin.de/~sgmd/) Arka (http://www.bioinformatics.org/genpak/)

14. Staden package with EMBOSS

15. EMBOSS/Jemboss Jemboss is the new Graphical User Interface (GUI) to EMBOSS, designed to facilitate the use of programs. It is written in the programming language Java, enabling the interface to be used in both PC and UNIX environments.

16. EMBOSS/Jemboss The older Mac platform does not support this GUI, and only Macs running MacOS X can also run Jemboss. Web-start installed by default

17. EMBOSS/Jemboss The interface has been written at the HGMP-RC in collaboration with the EMBOSS team First release January 2002

18. EMBOSS/Jemboss A web launch tool (Java Web Start) must be installed on the client (i.e. user's computer) before Jemboss can be accessed to allow this Java program to be downloaded and launched from the web

19. EMBOSS/Jemboss The Jemboss server has been installed under linux, AIX, MacOSX, irix, Solaris and HP-UX. The server setup is very much dependent on the local environment and the level of security necessary for a site.

20. EMBOSS/Jemboss It is possible to set up a basic non- authenticated and non-encrypted server. This may be suitable for sites in which the server is only available internally. A more secure server can be set up which uses SSL for data encryption.

21. EMBOSS/Jemboss SOAP is used to communicate between the client and the server, Apache-Tomcat is used to deploy the Jemboss services.

22. EMBOSS/Jemboss

24. And now all this in practice! And now all this in practice!

25. Concluding remarks If you want to install Central server with system manager Pros and Cons of the EMBOSS package

26. The EMBOSS-Coktail jakarta-tomcat-*.tar.gz SOAP (Simple Object Access Protocol) Apache-x.x.tar.gz Libpng-tar.gz Z-lib.tar.gz EMBOSS-2..x.x.tar.gz The latest Java

27. EMBOSS minus The major deficiencies in the EMBOSS package are: BLAST, FASTA, ASSEMBLY You should use the publicly available software: Blast - NCBI, HGMP, many other sites Fasta - HGMP Assembly - Staden package

28. EMBOSS plus Much effort is put into removing arbitrary limits.E.g. Max. sequence length: 2Gb Many programs limited only by available memory Source code available for inspection, change and writing your own programs EMBOSS is FREE! GNU Public License Open Source Software

29. THE END Questions?