1. International Training Course on Bioinformatics/Computational Biology Applied to Genome Studies. Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, Brazil, May 21 th - June 15 th, 2001. Purpose : Bioinformatics or Computational Biology plays a key role in molecular biology, genome sciences and post-genomics/ functional genomics. At this moment, developing countries have only minor contributions in this field, and it is thus of utmost importance to strengthen this capacity. BioInformatics is a fairly level playing field and has a direct impact on basic reasearch and on the development of new tools in biotechnology, and for disease control. However, training and support of resource centers are badly needed.

2. Course Objectives : To establish a "train-the-trainer" workshop in a multidisciplinary and international networking framework for bioinformatics/ computational biology, applied to pathogen genome research. A group of 20 people was to participate in theoretical and practical courses on medium and advanced level Bioinformatics applicable to pathogen genome research and prepare for teaching similar courses in their home country, at the same time promoting South-South and South-North interactions in computational Biology/Bioinformatics. Appropriate training material was to be prepared to assist in these courses, in the form of presentations and a course manual.

3. Local organizing Committee : External organisers/facilitators : Wim Degrave Chuong Huynh (NCBI) Claudio Struchiner Ashok Kolaskar (ATCC) Additional local staff and technical support : Leila de Mendonca Lima Antonio B. de Miranda Alex Amorim Jose Almeida Jonathas Scott External facilitators : Branch Oralee, NCBI, USAMulder Nicola, EBI, UK Carlton Jane, TIGR, USAMungall Chris, Univ of Calif. Berkely, USA Fischer Beth, Univ of Pittsburgh, USAOduola Ayo, WHO/TDR, Switzerland Garratt Richard, Univ. of SP, Brazil Quackenbush John, TIGR, USA Gruber Arthur, Univ. of SP, Brazil Sicotte Hugues, NCBI, USA Hide Winston, SANBI, South Africa Zingales Bianca, Univ. of Sao Paulo, Brazil Lawson Dan, Sanger Centre, UK

4. Target group and selection criteria : Twenty-one individuals (8 from Latin America, 5 from Africa, 6 from Asia, 2 from non- tropical disease endemic countries) were selected, from ~90 applications, based on the following criteria : 1. Doctoral and especially post-doctoral level students, with either : good biochemistry/molecular biology background and basic knowledge in (bio) informatics (e.g. use of internet, basics of unix/linux, general sequence analysis by computer), or with good (bio)informatics background and basic knowledge in biochemistry/molecular biology 2. Have permanent access to computers and a teaching facility, have access to regular e-mail and internet (www), be actively engaged in biochemistry, molecular biology, computational biology/bioinformatics or closely related research, and be fluent in english. 3. Send a detailed CV, a personal letter explaining the reasons for application and how you and your home institution/country will benefit from your participation. Also specify how you and your institution can collaborate in an international network for bioinformatics in genome analysis. Include a letter of recommendation from your Institutional Head. Also, 15 graduate students from Rio de Janeiro and São Paulo attended theoretical classes, 3 students also followed most of the practical sessions.

5. Facilities : Participants stayed at the Fiocruz Guest House "Casa Amarela", right across the computer facilities. Lectures were given from 8h30 -10; 10h30 -12h. Practical training was given from 13h30 -19h00, and exercises from 20h00 – 23h00 at the Programme for Scientific Computing (PROCC) facilities, Fiocruz. Lecture room for 50 people, with retro, slide and datashow projector Lecture room for practical sessions with 23 terminals (X, networked, ATM) Servers at PROCC/DBBM are composed of the following : SGI Challenge, 4 CPUs, 256 M RAM, 40 GB disk SGI Indigo II workstation SGI Origin 2000, 12 CPUs, 6 Gb RAM, 200 Gb disk SUN Enterprise E3500, 4 CPUs, 2 Gb RAM, 36 Gb disk SUN Sparc 1000, 8 CPUs, 512 Mb RAM, 25 Mb disk HPUX, 4 CPUs, 1.5 Gb RAM, 80 Gb disk

6. Programs Installed and used : Blixem_MSPcrunch Hiseg EMBOSS-1.11.0, GCG and Staden NCBI Toolkit ACT Mysql ArtemisCoils Clustalw1.7CAP3 Hmmer-2.1.1Repeatmasker InterProAlfresco IprScanSeals TRNAscan-SE-1.21Stackpack Wise2.1.23CAGREP BlastBelvu.SGI Phred/Phrap/Consed SPDBV, Rasmol Python-2.1, PERL

7. Course program. Week 1 : Fundamentals in Bioinformatics and basic nucleotide/protein sequence analysis Opening sessions, operating systems, networking, statistics, fundamentals of sequence analysis, perl scripting, sequence comparison, web assisted sequence analysis, scientific grant writing. Week 2 : Large scale sequencing, assembly and annotation. Large scale sequencing projects, assembly, annotation, gene finding, Perl scripting, clustering analysis, grant writing, Protein structure and function, protein sequence analysis and annotation, Linux installation. Week 3 : Databases and functional genomics. Genome database construction, transcriptome analysis, genome annotation. Week 4 : Special topics and BioInformatics networks. Bioinformatics and drug/vaccine development, analysis of low complexity sequences, bioinformatics centers and network formation, comparative genomics, pathogen genomes.

8. Audio/visual aids, study material and on-line training. All lectures and some of the practicals were recorded on video/CD-audio by Chuong Huyng and will be made available shortly. All students received several books related to bioinformatics, which they could take home. Fiocruz (PROCC library) also received a set. Other books were available for consultation in hard copy or on-line during the course. Powerpoint presentations of lectures and text of practicals are available at the web-site for on-line training. A web site is being set up for on-line training and presentation of course material. It is currently hosted at http://www.dbbm.fiocruz.br/helpdesk. It will be linked to the web domain http://www.bioinfohelpdesk.org http://www.dbbm.fiocruz.br/helpdesk

9. Course evaluation (Students) - 1 : 24 students filled out the final evaluation form (21 registered students + 3) 7 had background in computer sciences, 13 in biological sciences, 4 in both. Questions were asked : "Too much for 5 days?"13 Yes, 8 No (N=21) (overall appreciation) "Adequeately timed?"6 Yes, 14 No (N=20) (overall appreciation) "Too much material?"11 Yes, 9 No (N=20) (overall appreciation) "Need more practical time?"13 Yes, 11 No (N=24) "Need more lecture time?"6 Yes, 17 No (N=23) "Will you be able to apply what you have learned in this workshop to your practice ?" 24 Yes (N=24) "Do you recommend this workshop to your colleagues?" 17 Yes, 6 No (N=23) [Some participants indicating "No" noted that : the course was too long (1), too advanced (1) or should be given in a modified format (2) ]

10. Course evaluation (Students) - 2 : "After the training course and receiving the audio/visual material, do you feel confortable training other individuals in bioinformatics and/or organizing courses in you home institution?"17 Yes, 5 No (N=22) [Several participants remarked here that they would need support from outside trainers, or informatics people to install/run programs, or that they would need further training if to go beyond basic courses] "Do you favor regional or international training courses?" [most participants favor both, and recognize their specificity and benefits] Instructors evaluation (overall; N=20) : average : 1 good : 4 very good : 9 very good to excellent : 5 excellent : 1

11. Overall rating of the training course (content, computer lab, time usage, presentation style, audio/visual aids, knowledge of presenters) (N=24) : average : 7 good : 6 very good : 6 very good to excellent : 3 excellent : 1 Rating of Bioinformatics Network planning meeting (N=15) : poor : 1 average : 8 very good : 4 excellent : 2 Training course rating : pooraveragevery good excellentN week 1 9 12 223 week 2 1 6 13 324 week 3 4 11 823 week 4 6 12 422 overall 12 1123

12. Additional suggestions from the students : 1. Considering the duration of the course (4 weeks), and the intensity (8h30-23h30), the facilities (guest house and computer lab) were too crowded and did not offer enough confort. 2. Participants had different backgrounds and different levels of knowledge, which was hard to harmonize during practical sessions. It would be advisable to have a one week leveling course first, with basic molecular biology, basic informatics etc. Or courses could be organized separately for people with biology or informatics background. 3. International courses are very interesting and have advantages for exchange, collaborations etc. Regional courses are more efficient, as it easier to select participants with similar level. 4. External teaching staff should harmonize the practical sessions, and work around common exercises. All practicals should be pre-run, and there should be more time for individual study and going through exercises.

13. Recommendations for future courses Courses should not be too exhaustive, and number of participants and external facilitators should be limited. Time is needed for participants and local staff to absorb new knowledge. Ideally, participants should be able to work around a common theme (assignment) for the duration of the course (and maybe beyond?), where external facilitators work with the group on different aspects. Selection of students should be done differently. For “train-the-trainer” courses, participants should have gone through a basic or regional course.

14. Reflections/recommendations for the training programs There is a clear need for bioinformatics training courses at different levels: a) Basic level for general users, problem oriented. Ideally, such training is coupled to graduate training. Students should come in contact with both informatics and biology aspects. b) Medium and advanced level for : advanced tool users and for tool developers. Regional courses and training centers are best, as it is possible to select more homogeneous groups of students, who benefit maximum. Courses should not be overcharged, but be more oriented and leave enough time for study and collaboration (e.g. group work etc.) c) International courses could focus on "train-the-trainer" aspects, and focus on teaching techniques and materials, and development of course programs. The development of audio/visual and on-line material is very important, and helps the new trainers in their teaching activities. d) Short “Overview” course for program managers.

15. Issues to be resolved : 1. Is there a long-term commitment from WHO/TDR with the regional training centers? Timeframe, funding level ? 2. Is there a need for the International Center in the program? 3. The regional training centers should define (freely) on the level of courses they want/can organize, and whether their course should be general, or more specialized etc. Courses can vary in level, clients, and focus from one year to another. 4. Training centers should be free to organize follow-up of their students, and decide on the format. 5. Development of course material, book etc. should be continued. 5. WHO/TDR initiative should be interacting with other initiatives in the regions.