Bioinformatics World    

Site Journal

"What's new on Bioinformatics World ?"

Site Journal

This section is intended to keep you informed about latest additions and news at the "Bioinformatics World" pages. Because of the growing size of this portal, it may be useful to regularly check this site, in order to quickly identify sections which were updated recently. This site was started on September 30, 2003.          

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Oct. 11, 2006: ESTexpress and SAGEexpress (formerly collected as "ECexpression") are the expression data viewers of the portal ECgene, developed at Ewha Womans University, Seoul, Korea. These tools utilize the extensive expression data from EST and SAGE sources to develop a queriable expression ontology. A description was added to the ECgene chapter in section "ESTs, Splicing, Polyadenylation". The previous "ECexpression" entry was deleted.
     
October 2006          
Sep. 27, 2006: WORDCOUNT is an EMBOSS tool which counts words of a specified size in a DNA sequence. A description was added to main section "DNA Properties".
Sep. 19, 2006: Addition of several programs in the field of multiple sequence alignment (main section "Multiple Alignment"), in particular additional ClustalW servers (like ClustalW-XXL at EMBnet.ch), Jalview, MUSCLE and TCoffee. FAQ SIM3 was updated accordingly.
     
September 2006                               
Aug. 22, 2006: Complete check of all pages for broken links.
Aug. 22, 2006: Several new entries within the main page "TOP Sites", including the Kyoto University Bioinformatics Center, SANBI (South African National Bioinformatics Institute), and the Weizmann Institute of Science. In addition, a link to the new NAR Web Server Issue of July 1, 2006 was included.

August 2006      

July 2006         
Jun. 27, 2006: Update of GOTM in main section "GO Data Mining".
Jun. 27, 2006: Update of the Reactome description in main section "Pathways and Interaction Databases", especially concerning the tool SkyPainter, which can be used to graphically visualize "over-represented" pathways which are turned on by a given set of genes. FAQ PATH1 was updated accordingly.
Jun. 27, 2006: Update of the DAVID description in main section "Integrated Functional Data Mining", in particular concerning the "ID Conversion tool". FAQ DAT6 was updated accordingly.
Jun. 26, 2006: Extensive update of the KEGG description at main section "Pathways and Interaction Databases". Among others, a new entry was added, KegArray. KegArray is a standalone Java application for integrated analysis of gene expression profiles together with KEGG pathways and KEGG genomes.
Jun. 18, 2006: Expression Profiler: Next Generation (EP:NG) is the new version of the popular package for microarray cluster analsis of the EBI, providing the full functional range from the old version and additional features, together with a "unified" user interface. A description was added to main section "Microarray Data Analysis", as well as to FAQ EXP7.
Jun. 17, 2006: Update of the GEO - Gene Expression Omnibus description in main section "Microarray Data Repositories".
Jun. 14, 2006: Update of the HapMap description in section "SNPs, Mutations, Disease".
Jun. 13, 2006: Update of the descriptions of HGMD (Human Gene Mutation Database),  dbSNP, and OMIM in main section "SNPs, Mutations, Disease". In addition, the chapters "dbSNP IDs" and "OMIM IDs" in main section "ID Guide" were updated.
Jun. 4, 2006: NATURE Human Genome Collection is a supplement to the June 1, 2006 issue of Nature, collecting milestone articles of the road to the discovery of the human genome. A description was added as first entry to the new section "Human Genome Documentation" within main page "The Human Genome".

June 2006                    
May 30, 2006: Match, P-Match and Patch, which are part of the programs at BIOBASE portal of gene regulation, are designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. A description of these resources was added to main section "TFBS Matching". In addition, sections describing the databases TRANSFAC and JASPAR were updated. FAQ GEN2 was updated accordingly.
May 29, 2006: DBTSS - Database of Transcription Start Sites, maintained at Tokyo University, contains  information of the genomic positions of the transcriptional start sites and the adjacent promoters for most of the annotated human and mouse genes. The DBTSS description was updated in main section "Promoter Extraction" and in FAQ GEN6.
May 28, 2006: Eponine, developed at Sanger Institute, is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence. FirstEF (First Exon Finder), provided at Cold Spring Harbor Labs, is a 5' terminal exon and promoter prediction program. Descriptions of both programs were added to main section "Promoter Prediction". Other resources in this section were also updated, like Dragon Promoter Finder, NNPP, Promoter Inspector and Promoter Scan. Finally, FAQ GEN1 was updated accordingly.
May 17, 2006: Another update of FAQ STRUC1, now providing a more "structured" view of the topic.
May 16, 2006: MSD, the EBI Macromolecular Structure Database, is the European project for the collection, management and distribution of data about macromolecular structures. A description of MSD was added to main section "Structure Databases". FAQ STRUC1 was updated accordingly.
May 16, 2006: The wwPDB (world wide PDB) is a consortium which acts to maintain a single Protein Data Bank Archive of macromolecular structural data. A description of wwPDB was added to main section "Structure Databases". The chapters describing PDB, and MMDB were also updated.
May 15, 2006: Update of the PSORT description in main section "Proteins", and update of FAQ PROT6.
May 15, 2006: Extensive update of the descriptions of the resources SMART, PROSITE, and InterPro within the main section "Proteins".
May 14, 2006: iPfam is a resource that describes domain-domain interactions that are observed in PDB entries. PfamAlyzer, which is only available at the Karolinska mirror of Pfam, is a graphical user-friendly interface to Pfam. Descriptions of iPfam and PfamAlyzer were added to the Pfam chapter in main section "Domains, Families". The Pfam chapter itself was updated thoroughly. FAQs RET1, PROT1, and PATH3 were updated accordingly. 
May 9, 2006: Extensive update of the ClustalW and WebLogo descriptions at main page "Sequence Similarity". FAQs GRAPH1 and SIM4  were updated accordingly.
May 9, 2006: DbClustal is a protein multiple alignment program that aligns top scoring full-length sequences from a protein blast database similarity search. A description of DbClustal was added to main section "Multiple Alignment".
May 9, 2006: Update of the EMBOSS description in main section "Sequence Tool Collections", as well as extensive updates of main sections "Pairwise Alignment" and "Multiple Alignment".
May 9, 2006: Extensive updates within main section "Special Database Search", especially describing the programs BLAT and SSAHA.
May 5, 2006: Two BLAST programs have been added at the main section "Sequence Similarity": MegaBLAST and PHI-BLAST. FAQs SIM1, 2, 6 and GENOM2 were updated.
May 4, 2006: Renaming of the NCBI resource DART (Domain Architecture Retrieval Tool) to CDART (Conserved Domain Architecture Retrieval Tool) to conform to the NCBI website.
May 4, 2006: Extensive update of the descriptions of the BLAST and FASTA programs for sequence similarity search in main section "General Database Search", as well as of the PSI-BLAST chapter in main section "Special Database Search".
            
May 2006                        
Apr. 24, 2006: Minor updates within main section "Sequence Retrieval Resources".
Apr. 24, 2006: Update of the UniProt description in main section "Protein-centered Data Integration". In particular, a tool called ID Mapping was added, which is capable of converting lists of IDs (like GenBank AC, KEGG pathway ID, Gene name, or Entrez Gene ID) to and from UniProtKB ID or AC. FAQs DAT6 and PATH7 were updated accordingly. In addition, the chapter "UniProt IDs" was modified.
Apr. 21, 2006: Update of the RefSeq description in main section "General Sequence Databases", especially concerning data accessibility. In addition, the chapter "RefSeq IDs" was modified.
Apr. 20, 2006: Update of the GenBank description in main section "General Sequence Databases". Among other points, the 2 programs BankIt and Sequin, designed for sequence submission were added. In addition, the chapter "GenBank IDs" was modified.
            
April 2006                   
Mar. 30, 2006: Complete check of all pages for broken links.
Mar. 23, 2006: A new entry was added to the "ID Guide" (main section "Sequence Retrieval"), namely typical IDs from the Reactome database of biological pathways.
Mar. 20, 2006: Update of FAQ TOP3, describing the quick access to services provided by the major bioinformatics institutes.
Mar. 14, 2006: EEL - Enhancer Element Locator is a tool for locating distal gene enhancer elements in mammalian genomes by comparative genomics and to identify conserved TFBS in predicted enhancers. A description of EEL was added to main section "TF Module Matching" and to FAQs GEN4 and GENOM6.
Mar. 3, 2006: Extensive update of the section describing the UCSC Table Browser (main section "Human Genome Databases"), a powerful and flexible graphical interface for querying and manipulating the UCSC Genome Browser annotation tables. FAQs RET3 and HUMGEN1 were adapted accordingly.
Mar. 3, 2006: Update of FAQs EXP1 and EXP11, adding new reources of expression information, like in situ RNA image databases, and databases which store RT-PCR, Northern Blot, and Western Blot data. A new FAQ (EXP21) was created, respectively.
Mar. 3, 2006: Update of the section describing the portal MGI-Mouse Genome Informatics, now including the resources MGD, GXD, and MGS. Furthermore, a typical MGI accession entry was added to the "ID Guide".
Mar. 2, 2006: Extensive update of the section describing the UCSC Genome Bioinformatics portal at the main section "Human Genome Databases". Addition of new entries like "ENCODE at UCSC", and UCSC VisiGene. The latter site is a portal for viewing microscopic images of large-scale in situ hybridization projects. As a consequence, a new sub-section ("RNA Localization Databases") was created within main page "Expression" and a new FAQ (EXP20) was added. The following FAQs were updated: SIM1, HUMGEN1, and OTHGEN1.
Mar. 1, 2006: Update of FAQ INFO1 describing the most efficient ways to search the "Bioinformatics World" portal for any keywords of interest.
            
March 2006      
Feb. 23, 2006: PubReMiner is a tool for PubMed query building and literature mining, developed at the Academic Medical Center (AMC) in Amsterdam, Netherlands. A description of PubReMiner was added to main section "Literature Browsers", and two new FAQs (LIT3 and 4) have been added.
Feb. 22, 2006: HapMart is a data mining tool for retrieving data from the HapMap database, storing data on genetic variations like SNPs. A description of HapMart, together with an update of the HapMap description, was added to main section "SNPs, Mutations, Disease". FAQ GENOM1 was updated accordingly.
Feb. 17, 2006: Update of the sections describing the ENCODE project (within "Data Integration") and HiMAP (within ""Pathways and Interactions Databases").
Feb. 15, 2006: A new entry was added to the main section "ID Guide", namely an example ID for the Human Gene Mutation Database (HGMD).
Feb. 14, 2006: HiMAP is a dynamic browser for the human protein-protein interaction map, provided by the University of Michigan. HiMAP allows users to begin with a single protein or a set of proteins and explore both known and predicted protein-protein interactions. A description of HiMAP was added to main section "Pathways and Interactions Databases". In addition, FAQs PATH1 and PATH3 were updated.
Feb. 10, 2006: The CGAP portal described in main section "Cancer" provides also tools (SAGE Genie) in the field of SAGE tag count-based gene expression analysis. These tools can also be used to determine the reliability of individual SAGE tags for expression analysis of specific genes. A new FAQ (EXP19) was created describing this question. In addition, FAQs EXP1 and 11 were updated. Finally, a new FAQ (PATH7, RET11) was added, describing ways to retrieve gene lists of specific pathways for further data analysis.
Feb. 10, 2006: A new sub-section was created within "Various Tools" collecting useful links to Code Tables, like IUPAC nucleotide and amino acid tables, genetic code tables, and similar sites.
Feb. 9, 2006: Extensive update of the section describing the NCBI resource CGAP - Cancer Genome Anatomy Project within main section "Cancer". FAQs RET2, RET4, and PATH1 were updated. Two new FAQs (GENOM9 and 10) were created describing the expression analysis of a gene set of interest in cancer tissues and the comparison of normal vs. cancer profiles, respectively.
Feb. 9, 2006: The main section "Genomic Mapping, Cytogenetics, Cancer" was split in two sections in order to separate the cancer-related resources. Oncomine, which is a resource from the University of Michigan for examining gene expression in cancer, was added to this section.
Feb. 8, 2006: The Bookshelf is an NCBI resource which represents a growing collection of biomedical books that can be searched very similar to a PubMed query. A description of this site was added to the main section "Literature Browsers".
Feb. 7, 2006: A new FAQ page was created corresponding to the main section "Literature", and 2 new FAQs have been added. FAQ LIT1 describes tools which retrieve citations in other publications relating to own papers. FAQ LIT2 delineates the access to patent databases.
Feb. 7, 2006: Update of the sections describing the EBI, NCBI and Sanger Institute portals within "Top Bioinformatics Institutes". A new FAQ (TOP3) was added describing the quick access to services provided by the major bioinformatics institutes. A new FAQ (BIO1) was added listing bioinformatics-related discussion forums. The educational resources of the NCBI (Education, Science Primer) were added to the main section "Top Education".
Feb. 7, 2006: Restructuring of selected sections within the main index. Educational resources are now listed under "Top Education" within "Top Sites". Bioinformatics Journals are now contained in section "Literature". The section "Bioinformatics" was renamed to "Bioinformatics Development". FAQ BIO1 was migrated to TOP1.
Feb. 3, 2006: The "Alphabetical List" (A-Z) of all described resources is now directly accessible from the "Navigate" section at the start-page, thereby saving one click when selecting a specific site.
Feb. 2, 2006: Complete check of all pages for broken links.
Feb. 2, 2006: Pattern Search and Peptide Match are 2 resources provided at the PIR (Protein Information Resource) database. These programs are now described in main sections "Motifs 1 - Integrated Search" at the "Proteins" page and "Special Database Search" at the "Sequence Retrieval" page, as well as in FAQs RET1 and SIM2.
Feb. 1, 2006: BioCyc is a collection of Pathway/Genome Databases which describe the genome and metabolic pathways (NO signaling pathways !) of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms. The human database within BioCyc is called HumanCyc. A description of these resources was added to main section "Pathways and Interactions Databases". In addition, a respective section was added to the "ID Guide". Finally, a new FAQ (PATH6) was added which compares resources dealing with metabolic pathways, reactions and compounds.
            
February 2006                                         
Jan. 24, 2006: A new FAQ (PROT7, PATH5) was added describing how to explore which protein domains are present / overrepresented in a gene set of interest.
Jan. 23, 2006: Update of the description of WebGestalt within section "Integrated Functional Data Mining".
Jan. 3, 2006: A new NAR Database Issue has been made available online. A respective link was added to main section "Top Documentations".
Jan. 3, 2006: Minor update of FAQ EXP9 describing the submission procedure of microarray data to public databases like NCBI-GEO.
            
January 2006                     
Dec. 21, 2005: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. The PANTHER tools are very efficient for predicting the biological processes of gene datasets. A description of PANTHER was added to main section "Pathways", "Integrated Functional Data Mining" and to FAQs PATH1 and DAT8. In addition, a new FAQ (PATH4 = RET10) was created. Also, FAQ GENOM1 was updated with the cSNP analysis tool of PANTHER allowing the prediction of the functional impact of individual SNPs.
Dec. 20, 2005: HumanCyc is a bioinformatics database that describes the human metabolic pathways and the human genome. A description of HumanCyc was added to main section "Pathways", sub-section "Pathways and Interactions Databases".
Dec. 20, 2005: OBO - Open Biomedical Ontologies is an umbrella web address for well-structured controlled vocabularies for shared use across different biological and medical domains. A description of OBO was added to main section "Pathways", sub-section "GO Portals".
Dec. 19, 2005: WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of large sets of genes. A description of WebGestalt was added to main section "Pathways", sub-section "Integrated Functional Data Mining" and to FAQ PATH1.
Dec. 16, 2005: GOTM (GOTree Machine) is a web-based platform for interpreting microarray data or other interesting gene sets using Gene Ontology. A description was added to main section "GO Data Mining" and to FAQ PATH1.
Dec. 15, 2005: Addition of FAQ DAT8, describing the question how to produce a general annotation table for a gene set of interest.
Dec. 14, 2005: Complete check of all pages for broken links.
Dec. 14, 2005: The sub-section "Functions" within main section "Pathways, Interactions, Functions" was split into 5 sub-sections, which mainly reflects the diverse functionality of Gene Ontology (GO) based tools (browsing, annotating, data mining).
Dec. 14, 2005: PESTfind Analysis Webtool is provided by the Austrian EMBnet node and predicts PEST motifs as potential proteolytic cleavage sites in proteins. A description was added to main section "Proteins", "Motifs 3 - Modification".
Dec. 6, 2005: DAVID - The Database for Annotation, Visualization and Integrated Discovery integrates functional genomic annotations with intuitive graphical summaries. DAVID provides a comprehensive set of tools for investigators to visually summarize annotation from large list of genes, including those derived from microarray and proteomic studies. A description of DAVID was added to main section "High-Throughput Data Retrieval", and to FAQ PATH1. In addition, DAVID provides a very nice gene ID conversion tool, thus FAQ DAT6 was updated accordingly.
Dec. 6, 2005: HPR - Human Protein Atlas is a novel resource with the final aim to provide a complete catalog of the tissue distribution (normal, cancer) of all human proteins. Proteins can be simply searched via gene names. Data are presented as high-quality  immuno-histochemical images. A description of HPR was added to main section "Protein Localization Databases" and an example entry was added to the "ID Guide". In addition, FAQ PROT6 was updated accordingly.
Dec. 5, 2005: Update of the section describing BiblioSphere PathwayEdition of the Genomatix suite within main section "Pathways and Interactions Databases", and update of FAQ PATH1.

December 2005                    
Nov. 25, 2005: Two resources for siRNA design have been added to main section "Non-coding RNA", namely siDESIGN from Dharmacon, Inc., and siRNA selector from Wistar Institute.
Nov. 23, 2005: Update of the section describing the KEGG portal of pathway data within section "Pathways and Interactions Databases", and update of FAQ PATH1.
Nov. 23, 2005: Complete check of all pages for broken links.
Nov. 18, 2005: Repbase Update is the most commonly used database of repetitive DNA elements, like in the widely used program RepeatMasker. CENSOR is a software tool which screens query sequences against a reference collection of repeats (similar to RepeatMasker). A description of both resources was added to main section "Repetitive Elements" within "GENES". In addition, FAQ GEN3 was updated accordingly.
Nov. 18, 2005: Update of FAQ GENOM1 describing different approaches and resources for the retrieval of SNP (Single Nucleotide Polymorphism) data including the analysis of SNP-disease correlations. The SNP database dbSNP (NCBI) was added to the section "ID Guide" within main section "Sequence Retrieval".
Nov. 2, 2005: PicTar and TargetScan are resources which are used both for predicting the targets of a certain microRNA or for predicting the microRNAs which may target a specific mRNA of interest. These programs are now described  in section "Non-coding RNA" within main section "RNA". In addition, two new FAQs (RNA4 and 5) were added which address these topics.
Nov. 2, 2005: Examples of database entries for the resources Rfam and miRBase (see Oct. 31) have been added to the section "ID Guide" within main section "Sequence Retrieval".

November 2005                            
Oct. 31, 2005: Rfam and miRBase are the first two resources included in the section "Non-coding RNA" within main section "RNA", storing information on several types of non-protein coding RNA families. In addition, a new FAQ (RNA3) was created describing the question how to obtain data of regulatory non-coding RNAs.
Oct. 31, 2005: A new FAQ (PROT6) was added to FAQ section "Proteins" addressing the topic how to predict the subcellular localization of a protein of interest.
Oct. 28, 2005: A new sub-section was added to main section "Proteins" called "Protein Localization Databases", collecting all resources which store localization data based on laboratory experiments (images). The first entry in this section is GFP-cDNA, developed by EMBL and DKFZ. This is in contrast to programs which predict protein localization from sequence motifs.
Oct. 28, 2005: Update of the section describing the EMBL data integration-tool "Bioinformatic Harvester", located in section "Data Super-Integration".
Oct. 11, 2005: Update of the section describing iHOP-information Hyperlinked Over Proteins, which generates a network built of co-citations of genes and proteins in public literature. iHOP is contained in main section "Pathways and Interactions Databases".

October 2005          
Sep. 22, 2005: PolyA_DB, maintained at the University of Medicine and Dentistry of New Jersey (UMDNJ), is a database which provides several types of information regarding polyadenylation in mammalian species. These include polyadenylation sites and their locations with respect to the genomic structure of genes, cis elements surrounding polyadenylation sites, comparison of polyadenylation configuration between orthologous genes, and tissue / organ information for alternative polyadenylation sites. A description of PolyA_DB was added to main section "ESTs, Splicing, Polyadenylation".
Sep. 22, 2005: The section "ESTs and Splicing" in main section "Expression" was renamed to "ESTs, Splicing, Polyadenylation" in order to cover also this aspect of RNA processing and related data on tissue-specific expression.
Sep. 22, 2005: GenomeWeb, a huge portal of bioinformatics links which was provided by the Rosalind Franklin Centre for Genomics Research  (RFCGR) was shut down, therefore all related links were deleted. Somehow like a substitute, MedDB, created at the Medical University of Vienna, Austria, was added to section "Top Link Collections". MedDB provides a very good, concise, compact overview of bioinformatics resources, listed in well-structured categories. MedDB is especially useful if you want to get a quick-overview of resources in a specific field.
Sep. 16, 2005: Two FAQs (EXP15 and 16) have been added to the "Expression" section, addressing the matters of tissue-specific expression of alternative transcripts and contig generation from a set of EST sequences, respectively.
Sep. 14, 2005: Update of FAQ DAT2, now including the resource ECgene.
Sep. 14, 2005: Addition of several new microarray datasets to the section "Selected Microarray Datasets", especially in the context of endothelial cell biology and inflammation, hypoxia, and stress.
Sep. 13, 2005: ECgene (gene prediction by EST clustering) is a web portal from the Ewha Womans University, Seoul, Korea, which integrates alternative splicing information with EST and SAGE-based expression data. ECgene predicts genes by combining genome-based EST clustering and a transcript assembly procedure. There are several programs (ECgene Browser, ECfunction, ECexpression, ECprofiler, ASmodeler) which are all described at the ECgene section within main section "ESTs and Splicing".
Sep. 9, 2005: ATD - Alternate Transcript Diversity database aims to understand the mechanisms that are responsible for the formation of transcript isoforms on a genome-wide scale by creating a value-added database of full-length alternate transcripts from human and other model species. ATD is somehow an extended version of ASD - Alternative Splicing Database, which essentially covers only the matter of alternative splicing. A description of ATD together with its components AltTrans, AltPas and AltTss, was added to main section "Expression", sub-section "ESTs and Splicing". 
Sep. 9, 2005: ASD - The Alternative Splicing Database, maintained at the EBI, aims to understand the mechanism of alternative splicing on a genome-wide scale by creating a database of alternative splice events and the resultant isoform splice patterns of genes from human, and other model species. At the moment three databases are available: AltSplice,  AltExtron, and AEdb. A description of ASD was added to main section "Expression", sub-section "ESTs and Splicing". 
Sep. 8, 2005: ASG - Alternative Splicing Gallery, provided by the Bioinformatics Research Center at the North Carolina State University, uses an approach which integrates all transcripts derived from a gene into a single splicing graph to build a database of all human splice variants. A description of ASG was added to main section "Expression", sub-section "ESTs and Splicing".
Sep. 8, 2005: A new FAQ (DNA5) was added to FAQ section "DNA", describing the simple question of DNA translation and ways to display both DNA and protein sequence.
Sep. 7, 2005: The section "SAGE and ESTs" at the "Expression" page has been divided into 2 sections: "SAGE" and "ESTs and Splicing". The latter one now also contains resources which deal with matters of alternative splicing and transcript isoforms.
Sep. 7, 2005: ARED, the AU-Rich Element Database, stores information on adenylate-uridylate rich elements (AREs) in human mRNAs. ARED is maintained at the King Faisal Specialist Hospital & Research Centre (KFSH&RC) in Riyadh, Saudi Arabia. ARED contains GenBank entries where the 3'UTR matches the ARE motif, a 13-bp pattern which was computationally derived from a list of functionally labile ARE-containing mRNAs. A description of ARED was added to main section "RNA", sub-section "UTRs", as well as to FAQ RNA1.
Sep. 6, 2005: There will be a focus on building and structuring the main section "RNA". As a first step, resources in the fields of RNA structure prediction were added: Vienna RNA Package (including RNAfold, Alifold and RNAinverse), and some of the resources of the group of Michael Zuker (like the program Mfold). A new FAQ (RNA2) was created accordingly.
Sep. 2, 2005: A new sub-section was added to main section "Pathways" called "Enzymes", collecting all enzyme databases, like BRENDA, ENZYME, and IntEnz. Updates have also been added to the "ID Guide".
Sep. 2, 2005: The "shift" from EnsMart to BioMart (see Aug. 31) is now also described in several FAQs, in particular at the "DAT", "RET", "GEN", "GENOM", "HUMGEN", "EXP", "PROT", and "PATH" pages.     
     
September 2005               
Aug. 31, 2005: The well known data retrieval tool EnsMart has been largely replaced by BioMart. EnsMart originally was developed for the Ensembl genome database. Building on its success, BioMart, has now been applied to other biological databases. A description of BioMart as well as all related tools like Ensembl MartView, EBI MartView, WormBase MartView, and Gramene MartView was added to main section "High-throughput data retrieval" under "Data Integration".
Aug. 31, 2005: Two new FAQs (EXP13 and 14) have been added to FAQ section "Expression", describing specific features of CleanEx.
Aug. 30, 2005: CleanEx, provided by the Swiss Institute of Bioinformatics (SIB), is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons. A description of CleanEx was added to main section "Microarray Data Repositories" and to the "ID Guide". FAQs EXP1, 2, and 3 were updated accordingly.
Aug. 30, 2005: HUGO and HGNC have been added to main section "Human Genome". HUGO - the Human Genome Organisation is the international organisation of scientists involved in human genetics. The HGNC - HUGO Gene Nomenclature Committee approves a gene name and symbol (short-form abbreviation) for each known human gene.
Aug. 26, 2005: Update of FAQs DAT1, RET1, 2, 4, 5, PROT1 and PATH3.
Aug. 25, 2005: HPRD - Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. As a main focus of HPRD lies in protein-interaction data, the description of HPRD was added to section "Pathways and Interactions Databases". In addition, FAQs RET1, 2, 4, and 5 as well as FAQ PATH3 have been updated.
Aug. 24, 2005: iHOP - information Hyperlinked Over Proteins - generates a network built of co-citations of genes and proteins in public literature. iHOP is a public service provided by the Protein Design Group (PDG), National Center of Biotechnology (CNB), Madrid, Spain. A description of iHOP was added to section "Pathways and Interactions Databases".
Aug. 23, 2005: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. A description of IntAct was added to section "Pathways and Interactions Databases". FAQ PATH3 was updated accordingly.
Aug. 23, 2005: Update of the chapter describing the KEKK LIGAND database within section "Pathways and Interactions Databases". FAQs CHEM1 and CHEM2 were updated as well.
Aug. 23, 2005: ChEBI, Chemical Entities of Biological Interest, is a freely available dictionary of "small molecular entities". The molecular entities in question are either products of nature or synthetic products (like drugs). A description of ChEBI was added to section " "Small molecules databases" within "Cheminformatics".
Aug. 22, 2005: PharmGKB - the "Pharmacogenetics and Pharmacogenomics Knowledgebase", is a research tool developed by Stanford University, which correlates very efficiently data on genes, diseases, pathways and drugs. A description of PharmGKB was added to section "Small molecules databases" within "Cheminformatics". Also, FAQ CHEM1 was updated and a new FAQ (CHEM2) was created.
Aug. 19, 2005: Several databases were added to the new section "ID Guide".
Aug. 17, 2005: SkyPainter is a program which is part of Reactome, which can be used to graphically visualize "over-represented" pathways which are turned on by a given set of genes. A description of SkyPainter was included within the Reactome section at "Pathways Databases". FAQ PATH1 was updated accordingly.
Aug. 17, 2005: The japanese KEGG database is one of the major sites of information on metabolic and regulatory pathways. New KEGG-based resources were included in the KEGG section within "Pathways Databases": BRITE, KEGG ORTHOLOGY, and KAAS-KEGG Automatic Annotation Server. FAQ PATH1 was updated accordingly.
Aug. 17, 2005: Several databases were added to the new section "ID Guide".
Aug. 16, 2005: Several databases were added to the new section "ID Guide".
Aug. 12, 2005: A new sub-section was added to main section "Sequence Retrieval" called "ID Guide". Often, when reading publications or database entries, accession numbers appear where the user initially has no idea which database these IDs are derived from. The purpose of this section is to list typical IDs and accession numbers of important databases, which may help to identify others of the same type.
Aug. 12, 2005: Update of FAQs GEN4 and GEN5 with several resources described in the last days (OTFBS, SynoR, Target Explorer, and DBTSS).
Aug. 12, 2005: DBTSS - Search for TF Binding Site is a "sub-program" of the DBTSS database, allowing a whole-genome proximal promoter search for combinations of TFBS, also supporting user-defined patterns. A description of this resource was added to section "TF Module Matching".
Aug. 9, 2005: MOBS is a graphical tool for visualization of pre-specified modules of transcription factor binding sites in evolutionary conserved promoters of human genes. MOBS is part of the portal Dcode.org for comparative genomics and gene regulation. A description of MOBS was added to section "TF Module Matching".
Aug. 8, 2005: Target Explorer, a program from Columbia University, automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. A description of Target Explorer was added to section "TF Module Matching".
Aug. 5, 2005: SynoR performs genome-wide scans for clusters of evolutionary conserved transcription factor binding sites (cTFBS) in user-specified spatial configurations. SynoR is part of the portal Dcode.org for comparative genomics and gene regulation. A description of SynoR was added to section "TF Module Matching".
Aug. 3, 2005: MSCAN was developed at the Center for Genomics and Bioinformatics (CGB), a department of the Karolinska Institute. MSCAN is an algorithm that detects clusters of pre-specified transcription factor binding sites in genomic sequences (similar to Cluster-Buster). A description of MSCAN was added to section "TF Module Matching".
Aug. 3, 2005: OTFBS, developed at Institute of Bioinformatics, Tsinghua University, Beijing, is a method which can detect over-represented motifs of known transcription factors from a set of related sequences. A description of OTFBS was added to section "TFBS Discovery".
Aug. 3, 2005: The Zlab, located at Boston University, is led by Dr. Zhiping Weng, and develops programs in the fields of gene regulation and protein docking. Zlab also provides good linkpages to bioinformatics resources. Thus, Zlab was added to section "Top Link Collections".
Aug. 3, 2005: Cluster-Buster is already the third generation program (after Cister and Comet) developed at ZLAB for finding clusters of pre-specified motifs in nucleotide sequences. A description of Cluster-Buster was added to the section "TF Module Matching".
Aug. 3, 2005: A new sub-section was added to main section "Genes" called "Regulatory Unit Databases", which lists resources which store information on whole transcriptional regulatory units. TRRD (Transcription Regulatory Regions Database) is an informational resource containing an integrated description of the gene transcription regulation, meaning that for each gene, different data like promoters, enhancers, silencer, locus control regions, and individual transcription factor sites are included.
Aug. 1, 2005: The main section "Genes" was heavily re-structured in order to reflect the different purposes of programs and databases for regulatory sequence analysis. In particular, programs were categorized according to 3 types of motif: (single) transcription factor binding sites, combinations of TFBS (modules), and general motifs. In addition, programs were grouped together which match such motifs with target sequences, or which de novo predict such motifs from sets of target sequences. As consequence, the list of sub-sections in main section "Genes" was extended but hopefully it became easier to pick the appropriate resource for a special purpose.

August 2005               
Jul. 26, 2005: COMPEL and TRANSCompel are databases on composite regulatory elements affecting gene transcription in eukaryotes. COMPEL collects information about composite regulatory elements (CEs) - pairs of closely situated sites and transcription factors binding to them. A description of these databases together with the search tool CompelPatternSearch was added to main section "Promoter Analysis 2 - TF Modules" and to FAQ GEN2.
Jul. 25, 2005: Complete check of all pages for broken links.
Jul. 25, 2005: Minor update in main section "Promoter Analysis 1" and in FAQ GEN4, describing the program package RSAT, in particular concerning the modules "Genome-scale DNA-pattern" and "Genome-scale Patser".
Jul. 21, 2005: META PP allows a "one-button" submission of your protein sequence via a single-page interface to a variety of servers, for the purpose of secondary and tertiary structure prediction. A description of META PP was added to main section "Secondary Structure" and to FAQ PROT3.
Jul. 21, 2005: Cn3D, developed at the NCBI, is is a helper application for web browsers that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. The description of Cn3D was updated in main section "Visualization Software", and in FAQ STRUC1.
Jul. 20, 2005: Addition of several new sections at the "Main Index", like "Gene Regulation-centered Data Integration" within "Data Integration" (now containing resources like ElDorado or ENCODE, previously listed under "Promoter Analysis"), and " Promoter Analysis 2 - TF Modules" as well as "Selected TF-Target Databases" (describing the CREB Target Gene Database as the first entry) within "Genes". In addition, section "Promoter Analysis" was renamed to "Promoter Analysis 1 - Transcription Factors".
Jul. 14, 2005: A new FAQ (DAT6) was added to the section "Data Integration" describing options to convert lists of IDs (like microarray IDs) into other ID types (like gene names).
Jul. 14, 2005: Update of FAQ EXP2 listing another option to check if your gene of interest is contained on a particular microarray type, now including the resource UCSC Gene Sorter.
Jul. 14, 2005: Update of the text describing the resource EnsMart within the section "High-Throughput Data Retrieval".
Jul. 11, 2005: Back from vacation, update of my "Personal Publications" section, as the paper describing the TOUCAN software version 2.0 was released in the NAR web server issue of July.
        
July 2005
Jun. 16, 2005: Update of the TELiS description within section "Promoter Analysis" and FAQ GEN5. TELiS is a very fast and very easy-to-use system to find transcription factor binding motifs (TFBMs) that are over-represented in promoters of differentially expressed genes.
Jun. 15, 2005: Update of the microarray repository GEO of NCBI at the main section "Microarray Data Repositories", in particular adding a description of the thumbnail images of expression profiles that are displayed when performing Entrez queries. FAQ EXP3 was updated accordingly.
Jun. 14, 2005: Another public microarray dataset was added to the section "Selected Microarray Datasets", allowing to generate a "virtual multiple tissue Northern" for your gene of interest. It is called "Normal tissues of diverse types", produced at Stanford University. These data are available as GEO series record GSE2193. FAQ EXP11 was updated accordingly. Another public microarray dataset was added to the section "Selected Microarray Datasets", as the first entry in the field of endothelial cell development, describing the expression profilng of endothelial progenitor cells (EPCs) derived from peripheral blood. EPCs are compared to human umbilical venous endothelial cells (HUVEC) and CD14+ monocytes. FAQ EXP6 was updated accordingly.
Jun. 7, 2005: Update of FAQs RET2 and RET3 which address the general question of retrieving large sequence datasets in "whole-genome" approaches. In particular, the NCBI-Entrez descriptions were modified reflecting the new design of the Entrez query interfaces. Update of RET4 now including EnsMart as additional option to retrieve datasets of transcription factors expressed in certain tissues or cell types. Update of FAQs GENOM5 and GENOM7 describing the use of EnsMart to filter gene lists for those having a disease / SNPs context.
Jun. 6, 2005: The NCBI Entrez Genome Project database is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals from which all projects in the database pertaining to that organism can be browsed and retrieved. This database was added to the section "Multi-Species Portals" at the "Other Genomes" main page. In addition, pig (Sus scrofa) genome resources have been added to the section "Single Species".
Jun. 3, 2005: RSAT also provides programs to generate random datasets of sequences which can be used to verify the significance of results obtained by programs of Motif Discovery like Oligo-Analysis or programs of Motif Matching like DNA-Pattern. The programs Random-Genes and Random-Sequence are now included in the RSAT description within main section "Promoter Analysis" and are also cross-linked at the section "Sequence Randomization". In addition, a new FAQ (GEN10) was added addressing this question.
Jun. 3, 2005: A new sub-section was created at the "Genes" page called "Motif Design". This section collects programs which are designed to create a common motif from a set of (short) sequences, which is similar but still different from the section "Motif Discovery". The program Pattern-Assembly was added. This is a tool to assemble a set of oligonucleotides or dyads into clusters of overlapping patterns (the assembly). Pattern-assembly is part of the (RSAT) package of regulatory sequence analysis, which was created at the SCMBB, Brussels University. 
Jun. 2, 2005: RSAT has improved the functionality of its module of in-batch promoter sequence extraction, as it now supports upstream sequence recognition relative to the transcription start site and not only relative to the coding sequence (start ATG). This is an essetial prerequisite of high-throughput promoter extraction from mammalian genomes. This resulted in updates of the RSAT section in "Promoter Analysis" and in FAQ GEN6.
Jun. 2, 2005: Update of the UCSC Gene Sorter in main section "Gene-centered Data Integration" and in FAQ GENOM2. Update concerns several issues, like the possibility to choose between 3 options to sort a gene dataset by protein homology (BLASTP, Rankprop, PSI-BLAST). In addition, a new FAQ RET8 (=GEN9) was created, describing the question how to get the promoter/protein sequences of all proteins homologous to a query within a certain species.
Jun. 1, 2005: Entrez SNP is a part of the NCBI Entrez database system which incorporates the dbSNP database into Entrez. Thereby, SNP data can be queried using the same approach as the other Entrez databases such as PubMed and GenBank. Entrez SNP was added to the main section "SNPs, Mutations, Disease" and to FAQ GENOM1.
        
June 2005
May 31, 2005: GAD - Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. GAD is maintained by the NIH - National Institutes of Health. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data. A GAD description was added as first entry of the new main section "Disease-centered Data Integration". GAD can be used effectively to address specific questions, like described in FAQs GENOM5 and GENOM7.
May 31, 2005: Glovar is a project from the Sanger Insitute, which shows sequence variation (SNPs) in a genomic context. Glovar has an "Ensembl look-and-feel". A description of Glovar has been added to main section "SNPs, Mutations, Disease" and to FAQ GENOM1. In addition, the description of the VEGA Genome Browser was updated in main section "Human Genome Databases".
May 27, 2005: A new sub-section was created in main section "Genes", called "TF-Target Prediction". The section "TF-Target Prediction" contains programs which start with (mostly combinations of) TFBS and try to predict the promoters in a whole-genome approach where these "modules" could actually play a functional role. At the FAQ page, TF-target prediction is mainly discussed in FAQ GEN4. Also, there are overlaps with the more general question of "Motif Matching" and the programs in the respective section.
May 25, 2005: Update of the chapter describing the program ModuleScanner in main section "Promoter Analysis" and in FAQ GEN4. ModuleScanner, integrated in the TOUCAN package, performs genomic searches with a predicted CRM (cis-regulatory module) or with a user-defined CRM known from the literature to find possible target genes. ModuleScanner has been extended to screen pre-computed CNS (Conserved Noncoding Sequence) regions conserved between human and species like mouse, zebrafish, fugu or chicken. 
May 24, 2005: Addition of several resources of the commercial Genomatix suite for gene regulation analysis. DiAlign and DiAlignTF perform local multiple alignment and detection of conserved transcription factor binding sites (similar to MULAN-multiTF), and are described in the "Comparative Genomics" section and in FAQ GEN5. Further programs now described: SequenceShaper, FrameWorker, FastM and ModelInspector (section "Promoter Analysis" and FAQs GEN4 and GEN5), MatDefine (section "Motif Matching" and FAQ GEN2), SNPInspector (section "SNPs, Mutations, Disease"), and SMARTest (section "GenePrediction").
May 23, 2005: Whole Genome rVISTA (beta version) is a  site which provides access to the computational tool that allows for evaluation of which transcription factor binding sites (TFBS) are over-represented in upstream regions in a group of genes. This beta-version of the tool has been developed for the mm4 version of the Mouse genome. This tool is now included in the VISTA chapter within "Comparative Genomics", and in FAQ GEN5.
May 23, 2005: VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. Several improvements have been implemented in the VISTA package, which are now described in the VISTA section within "Comparative Genomics" and in FAQ GENOM6. These include the selection of different alignment programs in mVISTA, new mVISTA output modes like dynamic visualization in VISTA Browser, and rankVISTA, a new method to evaluate the statistical significance of an aligned region.
May 20, 2005: The Rhesus monkey (Macaca mulatta) genome is now available as preliminary version for BLAT search at UCSC. Update of "Other Genomes", "Single Species".
May 20, 2005: The VEGA (Vertebrate Genome Annotation) database is a central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence, provided by the WTSI - Wellcome Trust Sanger Institute. VEGA is tightly linked to the Ensembl project. A description of VEGA was added to the main section "Human Genome Databases" and to FAQs HUMGEN1 and OTHGEN1.
May 19, 2005: Update of FAQ GEN2 describing resources to predict transcription factor binding sites in promoter sequences. In particular, also programs which allow to search for individual TFBMs and to search for user-defined patterns or profiles have been added.
May 18, 2005: TELiS (see May 10, 2005) now provides the option to analyze a gene set from a microarray analysis not only using the TRANSFAC database of transcription factor binding matrices but also the open-access JASPAR database. The TELiS description was updated in main section "Promoter Analysis" and in FAQs GEN5 and GEN7. In addition, a second JASPAR website was included which allows different queries, similiar to the "Query Transfac" options. Therefore, the section describing JASPAR at the main page was largely extended.
May 17, 2005: ECR Browser is a powerful tool to analyze multi-species genomic alignments. Now, there is a feature to submit aligned regions from ECR Browser to MULAN / multiTF to detect multi-conserved transcription factor binding sites. The respective sections in "Comparative Genomics" as well as FAQs GEN5 and GENOM6 were updated.
May 17, 2005: PLoS Computational Biology is a monthly, peer-reviewed open-access publication starting June 2005, as one of the high-quality opnen access journals from the Public Library of Science (PLoS). A description was added to the section "Bioinformatics", "Journals".
May 17, 2005: DOAJ - Directory of Open Access Journals is a service which covers free, full text, quality controlled scientific and scholarly journals. DOAJ was added to the main section "Journal Browsers".
May 13, 2005: Although this web portal has reached a significant size, there was no section yet describing the principal sequence databases which are used by many tools and programs. Examples include GenBank, Ensembl, CCDS, RefSeq, Swiss-Prot and TrEMBL. It is essential to understand the basic architecture of these databases, the ways to access the data, and the "look" of individual accession numbers. Therefore, a new sub-section ("General Sequence Databases") was created in section "Sequence Retrieval" collecting this information. In addition, the program Dbfetch was added, which provides an easy way to retrieve entries from various databases at the EBI.
May 12, 2005: PrimerBank is a public resource for PCR primers, developed at Harvard Medical School. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank was added to main section "Primers and In silico PCR", as well as FAQ DNA1.
May 10, 2005: TELiS is a very fast and very easy-to-use system to find transcription factor binding motifs (TFBMs) that are over-represented in promoters of differentially expressed genes, as retrieved from microarray analyses. The TELiS database has been included in main section "Promoter Analysis" and in FAQs GEN5 and GEN7.
May 2, 2005: Genomatix is a company based in Munich, Germany, which offers databases and services aimed at understanding gene regulation at the molecular level. Some additional (commercial !) Genomatix resources have been included at specific sections, like the GPD - Genomatix Promoter Database (section "Promoter Extraction"), and BiblioSphere PathwayEdition (section "Pathways and Interactions Databases").
        
May 2005                
Apr. 28, 2005: Update of the description of the European Patent Office (EPO) within the main section "Patent Databases".
Apr. 21, 2005: A new section was added to the main page called "Cheminformatics", which covers resources storing and managing data on small organic molecules. The NCBI resource PubChem was added as the first entry. As example, PubChem can be used to gain information on structure and biological activity of substances like "Aspirin" or "Celebrex". A corresponding question (CHEM1) was also added to the new FAQ page "Cheminformatics".
Apr. 14, 2005: Update of the section "Personal Records" with a brief text describing the establishment of an efficient "interface" between the lab scientist and the world of bioinformatics tools and databases as my personal bioinformatics "philosophy". In addition, a sub-chapter "What others say" was added, listing some of the feedback that users gave when using this web portal.
Apr. 12, 2005: A new section was added to the main page called "Proteomics", which will cover resources in this expanding field. The first entry of the sub-section "Selected Proteomics Datasets" is "Vascular Proteomics", a web site provided at the Department of Cardiovascular Medicine, St George's Hospital Medical School, University of London.
Apr. 6, 2005: Update of FAQ RET1 which deals with the question to identify all proteins which contain a certain domain or motif in their sequence. Similar to the NCBI resource DART, the EMBL database SMART can be used effectively to screen for proteins of similar domain composition as your query sequence.
Apr. 5, 2005: FAQ GENOM2 analyses different approaches to detect distant homologs of a gene / protein of interest. This FAQ was extended by a group of programs designed to detect weak homologies via multiple sequence alignments. In particular, the following resources have been included: PSI-BLAST (NCBI), BlastView (EBI), and a series of programs available at the BLOCKS server (Block Searcher, IMPALA, RPS-BLAST, Block Maker, Blocks Multiple Alignment Processor, LAMA, and COBBLER).
Apr. 5, 2005: Update of ClustalW, a program which produces multiple sequence alignments of protein sequences, both at the main page "Sequence Similarity" and in FAQ SIM3. 
Apr. 4, 2005: TRANSFAC is the most important database storing information on transcription factors and their binding sites. The public versions of TRANSFAC databases are not only searchable at the German site BIOBASE but also provided by public SRS servers. This "how to..." is now contained in the TRANSFAC chapter at the main "GENES" page, as well as in FAQ GEN7.

April 2005             
Mar. 31, 2005: Update of the program ECR Browser in section "Comparative Genomics" and FAQ GENOM6, which now provides the feature to display pre-computed conserved transcription factor binding sites directly in ECR Browser, without having to run "Grab ECR" and rVISTA first.
Mar. 29, 2005: Update of the NCBI-resource BLink (Blast Link) within "GENOMICS" describing the connection between BLink and HomoloGene. FAQ "GENOM2" was modified accordingly.
Mar. 18, 2005: Update of FAQ GEN4 concerning the description of the program DNA-pattern (RSAT), which can be used to screen sequence data sets for known patterns like transcription factor binding sites.
Mar. 2, 2005: Update of the TOUCAN chapter in main section "Promoter Analysis" by adding the alignment programs LAGAN and BLASTZ.
Mar. 1, 2005: The LAGAN Alignment Toolkit is a set of alignment programs for comparative genomics. The three main components are a pairwise aligner (LAGAN), a multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All 3 are based on the CHAOS local alignment tool. Descriptions of these programs have been added to the main section "Comparative Genomics".

March 2005           
Feb. 17, 2005: Complete check of all pages for broken links.
Feb. 17, 2005: The process of layout update of the Bioinformatics World-portal is finally completed. All tables now show 2 instead of 3 columns, as the third column gradually lost importance and functionality. In addition, table width now is dynamically adapted to the individual user's browser and screen resolution, as tables now always cover the whole browser window (and not less or more space). Finally, font size of text within the "Main Index" tables was increased to the size used also at the "FAQ" pages, as the font size previously used was hardly legible at "modern" screen resolutions like 1280x1024 pixels, which is often used by TFT monitors.

February 2005  
Jan. 26, 2005: Restart of work for the Bioinformatics World-portal after several weeks of major internal reorganization due to a relocation of the institute to a different district in Vienna.

January 2005   
Dec. 22, 2004: The main section "Nucleic Acids" was divided into 2 main sections now called "DNA" and "RNA". Likewise, the corresponding FAQ section was split, and the pre-existing FAQs NUC1-4 were renamed to DNA1-4. All links were updated.
Dec. 21, 2004: The UCSC program Protein Duster removes formatting characters and other non-sequence related stuff from a protein sequence. A description was added to the main section "Various Tools".
Dec. 21, 2004: The UCSC Proteome Browser Gateway provides a fast access to protein - specific data for a gene of interest. Descriptions of this resource have been added to main section "Data Integration" and to FAQ DAT1.
Dec. 2, 2004: The MAR-Wiz tool, provided by Futuresoft Corp., aims at discovering the presence of Matrix Association Regions, or MARs, within DNA sequences. A description of MAR-Wiz was added to the main section "Gene Prediction" within "Gene Analysis".

December 2004         
Nov. 30, 2004: Google Scholar is a novel Google service which can be used very effectively as citation tracking service, as publications which were cited by others show a link to these references. A description of this program was added to the main section "Literature".
Nov. 26, 2004: Update of FAQ GEN4 with detailed descriptions of programs for Motif Matching, together with explanations of the differences between consensus-based (or pattern-driven) and profile-based (or alignment-driven) methods. In addition, the EMBOSS program FUZZNUC for motif matching was added to this section.
Nov. 25, 2004: A new sub-section "Motif Matching" was created within the section "Gene Analysis", collecting all programs which screen a set of sequences with a specific pattern, motif, or profile matrix. As new entry, the program Motif Matcher at UCSC was described.
Nov. 24, 2004: A new sub-section "Selected Pathways" was created within "Pathways, Interactions, Functions", listing selected databases of individual pathways or protein interaction networks. As first entry, the TNFa / NF-kB pathway published by Cellzome (Heidelberg, Germany) was described.
Nov. 24, 2004: A new sub-section "Selected Microarray Platforms" was created within "Expression Analysis", describing selected "topic-specific" arrays (in fields like inflammation, apoptosis, angiogenesis, and endothelial cell biology) which are also listed in NCBI GEO database. As first entry, selected GEArray products developed by SuperArray Bioscience Corporation were described.
Nov. 19, 2004: Update of FAQ GEN5, part B3 with some of the programs described in the main section "Motif Discovery".
Nov. 18, 2004: Update of the new section "Motif Discovery" with descriptions of a series of programs in this field, like AlignACE, ANN-Spec, GLAM, Improbizer, WeederWeb and YMF.
Nov. 15, 2004: A new sub-section "Motif Discovery" was created within the section "Gene Analysis", now collecting all (DNA and protein) motif discovery programs. The prediction of over-represented motifs is widely used in promoter analyses, hence there are also close relations between these two topics, which is now also demonstrated by the close "proximity" of these 2 sections.
Nov. 15, 2004: Addition of the RESID Database to the main "Proteins" page. The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications and cross-links including pre-, co-, and post-translational modifications.
Nov. 11, 2004: Update of the section "Webdesign" within "Informatics" including topics like Drop Down Menu creation and CSS (Cascading Style Sheets).
Nov. 11, 2004: A detailed description was added in the main section "Expression Analysis" how to query the microarray data repositories ArrayExpress (EBI) and SMD (Stanford Microarray Database) and how to download data. In addition, a new dataset was added to the section "Selected Microarray Datasets", concerning endothelial cells and Kaposi sarcoma. Likewise, FAQs EXP5 and EXP6 were updated.
Nov. 8, 2004: Relaunch of Bioinformatics World after several weeks of redesign and restructuring. The most important addition is a complete alphabetical index ("A-Z" button) of all resources which are described within the "Main Index"-pages. This means that now, searching for a specific tool or program is a very easy task. As another consequence, there is now only ONE main section for each resource, whereas before many resources were "scattered" over several pages. In addition, the site-specific search functions, powered by Google and Yahoo are still available ("magnifying glass" button), allowing to search for ANY keyword of interest. Both functions are provided at the "Navigate Bioinformatics World" section at the start site ("steering wheel" button). These link-buttons have also been added to all pages of the "Main Index" and the "FAQ Center", allowing a quick and easy navigation between these sites. During this process, also a complete check of all pages for broken links was performed.

November 2004    
Oct. 12, 2004: Complete check of all pages for broken links.

October 2004                         
Sep. 30, 2004: Additions of several "Selected Microarray Datasets", in the fields of endothelial cell biology (angiogenesis), inflammation (inflammatory bowel disease), and immunology (T cell activation). FAQ EXP6 was updated accordingly.
Sep. 29, 2004: Minor update in FAQ GENOM6 describing additional features of the program ECR Browser, which is a powerful tool in the field of comparative genomics.
Sep. 22, 2004: ModuleScanner is one of the programs integrated in TOUCAN, and it performs genomic searches with a predicted cis-regulatory element or with a user-defined combination of elements to find possible target genes. Updates have been made in main section describing TOUCAN ("Promoter Analysis") and in FAQs GEN4 and GEN5.
Sep. 16, 2004: Minor update in main section "General Freeware" adding portals for software download.
Sep. 10, 2004: The Chimpanzee (Pan troglodytes) was included as additional species at the main section "Other Genomes".
Sep. 10, 2004: multiTF is a novel tool which identifies transcription factor binding sites conserved across multiple species (similar to rVISTA which is restricted to the analysis of 2 sequences, meaning 2 species). MULAN is a multiple alignment program which is used prior to multiTF. Both resources, multiTF and MULAN are described in main section "Genomics", "Comparative genomics", as well as in FAQ GEN5 / GENOM3.
Sep. 9, 2004: CREME, which is part of the Dcode programs provided by the Lawrence Livermore Nat. Lab, is a web-server for identifying and visualizing cis-regulatory modules in the promoter regions of a given set of potentially co-regulated human genes. Descriptions of CREME have been added to main section "Promoter Analysis", and to FAQ GEN5.
Sep. 7, 2004: The main section "Genomics", "Genomic Mapping", was extended to cover also the topics "Cytogenetics" and "Cancer", and the the two NCBI - based resources CGAP (Cancer Genome Anatomy Project) and CancerChromosomes, a new ENTREZ database, were included.
Sep. 7, 2004: BLink (BLAST Link) is an extremely useful source of information concerning protein homologs and orthologs across multiple species. BLink is not available as "program per se" but as link in each protein record stored in NCBI Entrez. BLink descriptions have been added to main section "Genomics", "Phylogenetics" and to FAQs GENOM2 and STRUC1.
Sep. 7, 2004: A new FAQ (SIM6) was added to the section "Sequence Similarity", describing how to match a query sequence very quickly with a whole-genome assembly (related to the Sep. 2 entry concerning main section "Special Database Search").
Sep. 6, 2004: A new sub-section was created within main section "Genomics", dealing with genomic mapping, and the NCBI resources e-PCR and UniSTS have been included as first entries. UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments.
Sep. 6, 2004: A new FAQ (NUC4) was added to the section "Nucleic Acids", describing the program "In silico PCR" of UCSC, allowing the fast matching of PCR primer pairs with whole genome assemblies.
Sep. 2, 2004: A new sub-section of "Sequence Similarity" was created called "Special Database Search", describing special cases like the fast search of nearly exact matches, or (the opposite) remote homology detection, or the matching of short sequences (oligos, peptides) to genome assemblies. Likewise, the section "Primers" (within "Nucleic Acids") was extended to cover also programs dealing with "In silico PCR".
Sep. 1, 2004: STRING is an EMBL-database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations. A description of STRING was added to the main section "Pathways, Interactions", as well as to FAQ PATH3.
Sep. 1, 2004: The Bioinformatic Harvester, available at EMBL, is a kind of "data super - integration" tool, as it provides information from alreday "integrative" databases (like SOURCE, Ensembl, UCSC, and NCBI Entrez,...) together with additional predictions (like cellular localisation) in ONE SINGLE webpage. A detailed description was added to the main section "Data Integration" and to FAQ DAT1.
Sep. 1, 2004: A new FAQ (TOP1) was added to the section "Top-Sites" on how to find concise literature describing databases and web servers currently available.

September 2004                                   
Aug. 31, 2004: The main section "All-in-one Analysis" was merged with the section "Data Integration", in order to list collectively all sources for data retrieval and integrated data analysis packages. Therefore, the section "Data Integration" was split into several sub-sections, which allows the quick access to programs for e.g. gene-centered information or programs for high-throughput annotation and sequence retrieval.
Aug. 31, 2004: TOUCAN is a program for regulatory sequence analysis of clusters of genes. A new version of TOUCAN (V2) was released which shows some very useful improvements like the batch retrieval of e.g. human promoters along with their homologous mouse and rat counterparts. Therefore, the TOUCAN description was updated in main section "Gene Analysis", "Promoter Analysis", as well as in several FAQs in FAQ section "Gene Analysis".
Aug. 20, 2004: NCBI GEO Dataset records of microarray data now also provide options to display pre-computed clusterings of datasets, via the links "Data Analysis" and the cluster-thumbnail image within the GDS records. Therefore, the GEO description in main section "Microarray Data Repositories" was updated accordingly.
Aug. 20, 2004: The GNF Expression Atlas (Novartis) is at present the best global transcriptome analysis from human and mouse. The GNF atlas version 2 is now also available as NCBI GEO Dataset records, which led to updates in main section "Selected Microarray Datasets", and in FAQ section "Expression", questions EXP6 and EXP10-12.  
Aug. 18, 2004: A new portal of the Univ. of Tokyo to obtain open source clustering software for microarray data analysis was added to the main section "Expression", "Microarray Data Analysis". Cluster 3.0 is available for Windows, Mac, and Linux.
Aug. 16, 2004: A new FAQ (PROT5) describes programs for prediction of transmembrane regions, designed for single and multiple sequences, as well as multiple alignments as input.
Aug. 13, 2004: Update of programs for prediction of transmembrane regions in proteins (main section "Proteins", "Secondary Structure"), and adding an additional program named SOSUI.
Aug. 10, 2004: A new sub-section was created within the main section "Literature", describing databases storing documents of patents.
Aug. 9, 2004: Minor update of the section "Literature", separating "Literature Browsers" and "Journal Browsers".  

August 2004
Jul. 22, 2004: Complete check of all pages for broken links.
Jul. 20, 2004: Update of FAQ GENOM6 which describes programs to find Conserved Non-coding Sequences (CNS) in large genomic regions via comparative genomics. A direct comparison of the two programs mVISTA and zPicture was added.
Jul. 12, 2004: NAR (Nucleic Acids Research) published a new "web server issue" on July 1, and the corresponding link was added to the section "Top-Sites", "Top Documentations".
Jul. 12, 2004: New entry at the "Personal information" page, providing the reference of our new publication in ATVB describing the analysis of regulatory patterns of inflammatory gene expression from Interleukin-1-stimulated Human Endothelial Cells.
Jul. 12, 2004: The database "Genome KnowledgeBase" is an important resource of core pathways and reactions in biology. Recently, not only its name (and the URL) was changed to "Reactome", but the database and its interface were generally restructured. Therefore, minor changes have been made within the "Pathways" sections at the main and FAQ pages. 

July 2004
Jun. 16, 2004: Corresponding to the entry of June11, a new FAQ (GENOM6) was added to the section "Genomics", describing the identification of Conserved Non-coding Sequences (CNS) in large genomic regions via comparative genomics.
Jun. 11, 2004: Comparative Genomics is one of the most strongly expanding fields in bioinformatics, as more and more complete genome sequences become available. Therefore, this section within the main section "Genomics" was heavily updated. In particular, the description of the VISTA programs and related tools was extended. In addition, a new entry "Selected Comparative Genomics databases" was created, and the CVCGD, the Cardiovascular Comparative Genomics Database, was added as first example.
Jun. 2, 2004: Update of FAQ EXP2, now including the UCSC Browser as additional option to identify microarray probe sets corresponding to your gene of interest. In addition, for matters of clarity, the UCSC Gene Family Browser has been renamed to "UCSC Gene Sorter". Therefore, several main and FAQ sections have been updated accordingly.
Jun. 1, 2004: In order to cope with the exploding number of databases in the field of expression analysis, and especially microarray analysis, the main section "Expression, Pathways, Functions" was sub-divided into several sections. In particular, the new section "Selected microarray datasets" contains exclusively descriptions of individual datasets, in the fields of "global transcriptome analyses", "endothelial cell biology, "inflammation", and more. Several FAQs have been modified accordingly (DAT1, EXP1, 3, 4, 5, 6). The new FAQ EXP6 addresses specifically the question how to perform in silico profiling in the field of endothelial cell biology.

June 2004
May 21, 2004: Due to server restructurings at the University of Vienna, the new URL of "Bioinformatics World" is: http://homepage.univie.ac.at/herbert.mayer/ (the word "mailbox" was replaced by "homepage"). Anyway, old URLs are automatically re-directed to the new address.
May 21, 2004: A second version of the GNF gene expression atlas (Novartis) was released, describing the "normal, healthy transcriptome" of 79 human and 61 mouse tissues and cell lines. This is an additional valuable resource if you are looking for expression profiles of your genes of interest. Therefore, the main section "Microarray Resources", as well as the FAQs EXP11 and EXP12 were updated.
May 6, 2004: The widely known and used NCBI database LocusLink will be discontinued in 2004 and replaced by Entrez Gene. Entrez Gene maintains the full functionality (including the accession numbers) of LocusLink, but additionally providing all the useful features of Entrez-based databases (like field-restricted queries). This replacement provoked major and minor updates at the main section "Data Integration", as well as in FAQs DAT1, ALL1, GENOM1, EXP1, and GEN6. 
May 6, 2004: A new FAQ (GENOM5) was added to the section "Genomics" describing approaches to identify if a gene of interest is associated with a disease.
May 5, 2004: H-InvDB is a major new database hosted by the Japan Biological Information Research Center (JBIRC), with contributions from more than 40 institutes worldwide, like the german DKFZ. The scope of H-InvDB is to provide an integrative annotation of full-length cDNA clones available from high throughput cDNA sequencing projects. H-InvDB is therefore a valuable additional resource when looking for integrated data concerning your gene of interest (like Ensembl or SOURCE). Therefore, H-InvDB was included in main sections "Data Integration", "Human Genome", "Proteins" (Localization) and "Genomics" (Disease) as well as in FAQs DAT1, ALL1, GEN3 (repetitive elements), GENOM1 (SNPs), HUMGEN1, and EXP11 (virtual tissue Northern).

May 2004   
Apr. 23, 2004: Update of FAQ EXP11 ("virtual multiple tissue blot"), by adding GeneNote, a database of human genes and their expression profiles in healthy tissues (Weizmann Institute). GeneNote was also added to the section "Microarray Experimental Data" within the main section "Microarray Resources". The new FAQ EXP12 describes ways to identify sets of genes which are expressed in a specific cell type or tissue x-times higher than in another one (particularly demonstrated for endothelial cells).
Apr. 21, 2004: Update of FAQ EXP11, adding additional options to produce a "virtual multiple tissue blot" of your gene of interest.
Apr. 14, 2004: Major update of the databases COG (Clusters of Orthologous Groups of proteins) and KOG (the eukaryotic "pendant") within the main section "Genomics", "Phylogenetics". In particular, the NCBI CD-Search for conserved protein domains was extended to reveal also similarities to known COGs and KOGs. Accordingly, the FAQ GENOM2 was updated and a new FAQ (GENOM4, RET6) was added, describing the matter of retrieving protein data sets which are present in specific species while excluding others.
Apr. 6, 2004: Two questions (EXP10 and 11) have been added to the FAQ section, addressing the matters of how to look if a set of genes is expressed in a specific cell type, and how to get a "virtual multiple tissue Northern" of a gene of interest.
Apr. 1, 2004: Complete check of all pages for broken links.

April 2004
Mar. 31, 2004: As the number of sections within "Bioinformatics World" and thereby also the amount of text is constantly expanding, it became a matter of demand to provide a "Search this Site"-function, which was created by implementing the "site-specific" search functions of Yahoo and Google on top of the main index page. Accordingly, a new FAQ (INFO1) was added to the "Informatics" section, describing the differences between these 2 search engines and a lot of hints to exploit the full range of their options.
Mar. 26, 2004: Major update of FAQ EXP2 by adding EnsMart and ENTREZ GEO as additional options for the question how to identify microarrays containing your gene of interest, along with a minor update concerning the TIGR Resourcerer database. Minor update of the GEO description at the main page "Microarray resources", and at FAQs EXP1 to EXP5 reflecting the changes in navigating GEO, starting at the GEO homepage.
Mar. 23, 2004: The main section "Literature", "Archives" was updated by adding BioMed Central (BMC), a portal providing access to over 100 Open Access journals covering all areas of Biology and Medicine. The main section "Bioinformatics", "Journals" was heavily updated by adding a series of bioinformatics journals, like "BMC Bioinformatics", which provides FREE access to all articles.
Mar. 17, 2004: A new program was added to the section "Repetitive Elements" within "Gene Analysis". REPFIND is a program to find clustered, exact repeats in nucleotide sequences. REPFIND is especially useful to detect regulatory signals in 3'-UTR sequences of mRNAs. The FAQ GEN3 was updated accordingly. Likewise, a new FAQ (GEN8) was added to the section "Gene Analysis", analyzing the different strategies for a "whole-genome approach" to detect genes containing such signals in their 3'-UTRs.
Mar. 8, 2004: A new FAQ (GEN7) was added to the section "Gene Analysis" describing the different possibilities to quickly view the binding site profiles of individual transcription factors from TF databases. The FAQ GEN4 was updated accordingly.

March 2004
Feb. 26, 2004: The section "Pairwise and Multiple Alignment" within "Sequence Similarity" was split into the two logical sub-groups and both were updated especially by including many EMBOSS programs.
Feb. 26, 2004: Heavy update of the section "Sequence Manipulation" within "Various Tools", including many EMBOSS tools.
Feb. 25, 2004: For matters of clarity, the main section "Various Tools" was split into three sub-sections: Sequence Manipulation, Sequence Format Conversion, and Sequence Randomization.
Feb. 25, 2004: A new EMBOSS tool called Sixpack was added to the section "Translation" within "Nucleic Acids". Sixpack displays a DNA sequence with 6-frame translation and ORFs, and allows for selection of open reading frames that are larger than the specified minimum size. It is a quite potent tool as it provides direct links to related EMBOSS programs for follow-up analyses of the extracted ORFs. Also, a new EMBOSS tool called REMAP was added to the section "Restriction Sites".
Feb. 24, 2004: Update of the section "Motifs 4 - Localization" within "Proteins" by adding LOCtarget, a database of predicted subcellular localization of proteins, along with 2 organelle-specific databases ER-GolgiDB and NMP-db (a database of nuclear matrix associated proteins). In addition, the PSORT chapter was updated.
Feb. 24, 2004: Update of the section "Primers" within "Nucleic Acids" by adding the GenomeWeb linkpage covering sites dedicated to primer design, and by adding the CODEHOP program for designing degenerate primers from protein multiple sequence alignments. Accordingly, two new FAQs (NUC2 and NUC3) were created covering the topics of degenerate primer design and the "opposite case", the design of primers least conserved in a protein family.
Feb. 17, 2004: Update of the ENCODE project within the section "Promoter Analysis", describing the novel possibility to open a UCSC Genome Browser with a menu for selecting ENCODE regions.
Feb. 17, 2004: A new main chapter called "Promoter Extraction" was split from the table "Promoter Analysis" to group tools which are essentially concerned with the extraction of promoter sequences from databases (which is also clearly distinct from promoter prediction), and not with the prediction of transcription factor binding sites. In addition, PromoSer, a highly versatile tool for promoter extraction for human, mouse, and rat genes was added. The FAQ GEN6 was updated accordingly.
Feb. 16, 2004: Minor update at the FAQ RET5, concerning the matter of sequence retrieval via SRS (Sequence Retrieval System).
Feb. 6, 2004: Minor update at the TOUCAN-chapter in the section "Promoter Analysis", giving a concise explanation of the different orders of background models used in MotifScanner.
Feb. 5, 2004: Minor update at the GEO (NCBI)-chapter in the section "Microarray resources", concerning the description of the selection and comparison of subsets of sample records, now providing the feature to e.g. display a list of all the genes which show a min. 4-fold expression in one set compared to the other.
Feb. 2, 2004: JASPAR is an open-access database of transcription factor binding site (TFBS) profiles (PWMs) which was built from literature data, and is therefore "independent" from existing databases like TRANSFAC. ConSite is a web interface which allows the analysis of a query promoter sequence for potential TFBS stored in JASPAR. Therefore, ConSite and JASPAR were added to the main section "Gene Analysis", "Promoter Analysis". Likewise, the TOUCAN chapter was updated, now using not only the TRANSFAC but also the JASPAR profiles. In addition, FAQ question GEN5 was updated, describing that the so-called "Profile Comparison Tool" provided at the site of the JASPAR database can be used as additional option to check if an extracted sequence pattern corresponds to a known TFBS.

February 2004
Jan. 20, 2004: A new question (EXP9) was added to the FAQ section on "Expression, Pathways, Functions", dealing with the matter how to submit data of microarray experiments to public databases. In particular, the submission process to the GEO database (NCBI) is demonstrated.
Jan. 19, 2004: The main section "General Freeware" was updated to cover the most important freeware programs for the different fields, like office programs, image manipulation and administration, file recovery, file sharing and transfer, anti-virus protection, and firewall setup.
Jan. 14, 2004: A new sub-section "Forums" was added to the main section "Bioinformatics", and BioPlanet was included as the first entry. BioPlanet is one of the largest forums for discussing all sorts of bioinformatics related questions, from multiple alignments to open job positions, from training courses and seminars to the favourite programming languages used in bioinformatics. 
Jan. 12, 2004: The section "Microarray resources" within "Expression, Pathways, Functions" was updated by adding a link to MGED and MIAME. The Minimum Information About a Microarray Experiment (MIAME ) is a standard developed by the Microarray Gene Expression Data (MGED) group for the content of data which should be supplied when publishing microarray experiments.
Jan. 8, 2004: The main section "TOP Sites" was split into three sub-sections: Top Research Institutes, Top Link Collections, and Top Documentations. The new online database issue of NAR (Nucleic Acids Research) was added to the section "Top Documentations".
Jan. 7, 2004: Minor update of the main section "Comparative Genomics", separating diffferent tools (mVISTA / rVISTA, zPicture, ECR Browser, eShadow / PipMaker) provided by different institutes. Furthermore, eShadow, a new program for performing comparative sequence analysis of multiple closely-related nucleotide or protein sequences, was added to the section of the Comparative Genomics Center at Lawrence Livermore National Lab.

January 2004
Dec. 22, 2003: Complete check of all pages for broken links.
Dec. 22, 2003: There are several programs / algorithms for the alignment of syntenic genomic regions, like upstream regions (promoters) of a pair of orthologous genes. Examples include PipMaker, zPicture, and DBA. The main section "Sequence similarity", "Pairwise and Multiple Alignment" was updated with a section summarizing these programs.
Dec. 18, 2003: Heavy update of the main sections "Comparative Genomics" and "Phylogenetics". In particular, the VISTA package for displaying genomic alignments between different species was supplemented by additional programs (zPicture, ECR browser, PipMaker) with the focus on comparative analysis of regulatory regions. Furthermore, 3 additional programs for "Phylogenetic Footprinting" were introduced (ConSite, FootPrinter, PhyloCon). FootPrinter is also implemented in the TOUCAN workbench for regulatory sequence analysis, therefore the corresponding chapter (section "Promoter Analysis") was also updated. In addition, the FAQs GEN5 and GENOM3 were re-structured accordingly.
Dec. 17, 2003: UniProt was added to the main section "Data Integration". UniProt is a central database of protein sequence and function created by joining the information contained in TrEMBL, Swiss-Prot, and PIR.
Dec. 4, 2003: Major update of the section "GO-Gene Ontology" in the main section "Expression, Pathways, Functions", sub-section "Pathways, Interactions, Functions", especially concerning GO data retrieval via EnsMart. Accordingly, major revision of FAQ RET2 / EXP8 on how to "get all protein sequences from endothelial cells involved in inflammatory processes", stressing the two different approaches, via SRS / ENTREZ or via Gene Ontology (GO) assignments.
Dec. 3, 2003: New FAQs GENOM2 / PROT4 on how to search for orthologs and homologs of your gene / protein of interest, including the topic of protein families.

December 2003
Nov. 26, 2003: The NCBI database HomoloGene, which is a resource of curated and calculated orthologs for genes, was added to the main section "Genomics", "Phylogenetics".
Nov. 26, 2003: The database TIGRFAMs, which is complementary to PFAM, was added to the main section "Proteins", "Domains, Families".
Nov. 26, 2003: The main section "Other Genomes" was divided into the sub-sections "Multi-species portals" and "Single species", and thereby heavily updated..
Nov. 25, 2003: The description of the NCBI-OMIM database, which is a catalog of human genes and genetic disorders, was updated in main section "Literature", "Archives" and added to the new section "SNPs, Mutations, Disease".
Nov. 25, 2003: The main section "Genomics", "SNPs" was expanded to "SNPs, Mutations, Disease" to broaden its spectrum, and to include databases like HGMD, the Human Gene Mutation Database. HGMD is maintained by the Univ. of Wales and is the leading database storing not only mutations in human genes but also curated polymorphisms showing clear phenotypes. The FAQ GENOM1 was updated accordingly.
Nov. 25, 2003: The NCBI database AceView was added to the main sections "Data Integration" and "The Human Genome".
Nov. 17, 2003: Programs for prediction of protein disorder (DisEMBL, GlobPlot) were added to the main section "3D Structures", "3D Prediction". Likewise, the new FAQ STRUC2 was created to describe these programs and the reasons to use them.
Nov. 17, 2003: New FAQ PROT3 on how to perform structural predictions of your protein sequence of interest.
Nov. 17, 2003: The program pDRAW32 was added to the section "Graphical Tools". pDRAW32 is a downloadable freeware tool for plasmid drawing, available for Windows, Mac, and Linux.
Nov. 17, 2003: Major revision of the section "Proteins" at the main page. In particular, the prediction of short protein motifs was separated from the one of large globular domains. In addition, this topic "protein motifs" is now represented by several sub-chapters to quickly identify "integrated" (like the newly added database ELM, which has quickly developed into the largest collection of linear protein motifs) and specialized databases. The question PROT1 at the FAQ page was re-structured accordingly.
Nov. 10, 2003: Minor updates on FAQ questions EXP3 and EXP5, concerning microarray data on author's webpages.

November 2003
Oct. 23-27, 2003: Complete re-structuring of the whole "Bioinformatics World" portal, to facilitate access to the data. In particular, dissection both of the main page and the FAQ page into a series of individual but highly linked files. This action became necessary because of the growing size of these pages. In addition, this "Site Journal" was launched to keep you informed about latest news. 
Oct. 16-22, 2003: The section "Expression, Pathways, Functions" was updated, both at the main page and at the FAQs, also by introducing new questions EXP1, and EXP4, 5, and 7. The main purpose was to get both an overview how to access expression data for a gene of interest (microarray data, SAGE, ESTs), and in-depth information especially on public repositories of microarray data (like GEO, SOURCE, and Array Express).
Oct. 17, 2003: Comprehensive update on FAQ HUMGEN1, now describing the best "quick access" to the human genome data, including sequence search (graphical genome browsers), text search, and complex data mining. This also includes the first description of the new UCSC Gene Family Browser. Also, the corresponding section at the main page (Human Genome) was heavily updated.
Oct. 15, 2003: Update on MatInspector professional for FAQ GEN5.
Oct. 14, 2003: Update on MatInspector professional concerning the matrix similarity threshold, at the main page (Gene Analysis, Promoter Analysis) and FAQ GEN2.
Oct. 13-16, 2003: The re-structured NCBI-ENTREZ database was updated at the main page (sections "Data Integration" and "Sequence Retrieval") and several FAQ questions (RET2, RET3).

October 2003
Sep. 30, 2003: Complete check of all pages for broken links.

September 2003
Bioinformatics World was developed by Herbert Mayer, Medical University of Vienna, Austria (2001-2006)