Highlights & Achievements
New SLING-funded BiSSAP Version 1.2 software now available for download
Users of the SLING-funded BiSSAP (Biological Sequence Submission Application for Patents) software can now download the new Version 1.2. In addition to some new features, this update also contains minor technical corrections and some functional changes. Release Notes for BiSSAP Version 1.2
SLING-funded Bioinformatics Roadshows
During the SLING project, 33 Roadshows have been delivered to c. 1,100 PhD students, postdocs, staff scientists, Principal Investigators, industrial researchers, undergrads and Master’s students throughout Europe. View map of SLING Roadshows (locations indicated by blue markers)
EC signature to Grant Amendment No. 1
It has been agreed that the SLING project will be extended by six months (from 36 to 42 months, ending Aug 2012), with no additional funding. In addition, the original two 18-month reporting periods have been replaced by 18-month P1, 14-month P2, and 10-month P3. Annex I (Description of Work) has been revised accordingly.
3rd SLING Management Meeting
The third SLING Management Meeting was held at the EBI, Hinxton, UK
SLING Dissemination Events
To promote innovation in biotechnology, the European Patent Office (EPO) is collaborating with the EBI and the SIB to organize information seminars at the request of National Patent Offices, European universities, research institutes and biotechnological associations. An overview of biotechnological database resources (containing biological sequences published in scientific publications and in patents) are presented. Seminars highlight sequence search and comparison tools, as well as sequence filing tools to be published at the EBI or as biological patent sequences at the EPO. Workshops are given on participant's search questions given upon registration. The SLING dissemination website provides information on all the organized events. Please contact us if your organization is interested in hosting a seminar.
New SLING-funded BiSSAP Version 1.1 software now available for download
Users of the SLING-funded BiSSAP (Biological Sequence Submission Application for Patents) software can now download the new Version 1.1. In addition to some new features, this update also contains minor technical corrections and some functional changes. Release Notes for BiSSAP Version 1.1
SIB Data Services
The following achievements are directly dependent on continued support from SLING:
• Over 250 new enzymatic activities have now been defined in collaboration with the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology and in consultation with the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature
• Over 300 new enzymatic activities have now been annotated in UniProtKB/Swiss-Prot, providing users with enhanced coverage of known enzyme activities
• Coverage of protein structure space has improved with the annotation of almost 3,000 new literature references describing protein structures and the addition of over 14,000 new cross-references from UniProtKB to PDB
• Over 60 novel, newly-identified post-translational modifications have now been described using controlled vocabularies, and over 19,000 individual experimental post-translational modifications have now been annotated in UniProtKB/Swiss-Prot
SLING-funded Bioinformatics Roadshows
Between the start of the SLING project (1st March 2009) and 30th April 2011, there have been 21 SLING-funded Roadshows (with 8 scheduled from May to Nov 2011). To date, the SLING Roadshow user-training programme has reached several hundreds of people: c. 75% were PhD students or postdocs, with the remainder being staff scientists, Principal Investigators, industrial researchers, undergrads and Master’s students.
View SLING-funded Bioinformatics Roadshows in a larger map
New SLING-funded service to facilitate the filing of biological sequences
On the 31st Mar 2011, version 1.0 of the SLING-funded BiSSAP (Biological Sequence Submission Application for Patents) software went 'live' on the EPO website. BiSSAP facilitates the creation of sequence listings for patent applications containing biological sequences, and can be used to:
• prepare and verify sequences
• generate the sequence listing files for submission
• import existing sequence listings in WIPO ST. 25
• convert between sequence listing formats (WIPO ST. 25 and XML proposal)
• verify collections of sequence listings via a "batch verification" module
From user feedback questionnaires, only 47% of delegates had used SLING resources before the Roadshow in their country, compared with 60% pre-Roadshow usage before SLING, i.e. we have succeeded in reaching research communities that were not heavy users of the SLING resources. 97% would use the SLING resources after their Roadshow, indicating that the SLING Roadshows are effectively promoting the SLING resources to previously SLING-naïve researchers.
Access to EBI resources has been consistently metered using a real-time log-file analyzer to show web server usage patterns. Before SLING, the daily average web hits were c. 2.5 million (excluding Ensembl) and c. 3 million (including Ensembl). During the first 18-month period of the SLING project, the EBI hosted c. 1,704 million hits (excluding Ensembl) and c. 2,093 million hits (including Ensembl) from world-wide sources, i.e. daily average web hits have increased from c. 2.5 million to 3.3 million (excluding Ensembl), and from c. 3 million to c. 4.1 million (including Ensembl). The monthly average unique users has increased from c. 200,000 to c. 257,000, and the monthly average unique users making programmatic access (via SOAP and REST) has increased from c. 3,400 to 4,800. The annual number of programmatic jobs has greatly increased from c. 1 million to c. 20 million jobs.
The BRENDA database
Between the start of the SLING project (1st March 2009) and 28th February 2011, Systems Biology Markup Language (SBML) output functionality has been integrated into the BRENDA database. The BRENDA tissue ontology terms (and their respective definitions) have increased by c. 500. 140 new enzymes have been submitted to the International Enzyme Commission, and have been approved and integrated in the system of EC numbers.
SIB Data Services
Between the start of the SLING project (1st March 2009) and 28th February 2011, 109,516 annotated sequence entries have been added to UniProtKB/Swiss-Prot (now totalling over 519,000 entries). 50 types of post-translational modification (PTMs not previously annotated in UniProtKB/Swiss-Prot) have been added, and 18,256 of the 76,680 newly-annotated PTMs are based on experimental data. 143 new complete EC numbers and 123 preliminary EC numbers have been made available in UniProtKB/Swiss-Prot. Over 3,000 UniProtKB/Swiss-Prot entries have been updated according to the new enzyme information. Over 12,800 cross-references to PDB have been added to UniProtKB/Swiss-Prot, of which over 2,500 were manually verified, and relevant information annotated in the corresponding protein entries. In total, over 2,500 non-unique literature references (dealing with 3D-structures) were added to Swiss-Prot entries during this period.
SLING Mid-Term Review
The SLING Mid-Term Review was held at the EBI, Hinxton, UK
2nd SLING Management Meeting
The second SLING Management Meeting was held at the EBI, Hinxton, UK
1st SLING Management Meeting
The first SLING Management Meeting was held at the EBI, Hinxton, UK
SLING Launch Meeting
The SLING Launch Meeting was held at the EBI, Hinxton, UK