A universal Gene Ontology annotation, visualization
and analysis tool for functional genomics research

afp_go_tools

2008-08-03T19:34:38+02:00

@@ -1,5 +1,5 @@
- ===== Gene Ontology(GO) Tools for the Automatic Function Prediction(AFP) =====
+ ===== Gene Ontology(GO) Tools for Automatic Function Prediction(AFP) =====
  === Listing of 13 reviewed functional GO annotation tools available online ===
  
  {{ :go_annotation_tools.jpg?600 | Listing of 13 reviewed functional GO annotation tools}}

b2g_in_papers

2010-08-28T17:22:11+02:00

@@ -11,8 +11,10 @@
  {{:citas0810.png|donde nos citan}}
  \\
  \\
  **2010**  \\
+      - Popesku, JT and Martyniuk, CJ and Denslow, ND and Trudeau, VL and Laudet, V., PLoS ONE, Rapid Dopaminergic Modulation of the Fish Hypothalamic Transcriptome and Proteome, e12338 (2010). \\
+      - Studer, B. and Kolliker, R. and Muylle, H. and Asp, T. and Frei, U.C. and Roldan-Ruiz, I. and Barre, P. and Tomaszewski, C. and Meally, H. and Barth, S. and others, BMC Plant Biology, EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass(Lolium spp.) (2010) \\
       - Jørgensen T.R., Nitsche B.M., Lamers G.E., Arentshorst M., van den Hondel C.A., Ram A.F., Appl Environ Microbio, Transcriptomic insights into the physiology of Aspergillus niger approaching a specific growth rate of zero (2010) \\
       - Heimel K, Scherer M, Vranes M, Wahl R, Pothiratana C, Schuler D, Vincon V, Finkernagel F, Flor-Parra I, Kämper J., PLoS Pathog, The Transcription Factor Rbf1 Is the Master Regulator for b-Mating Type Controlled Pathogenic Development in Ustilago maydis, 6, pii: e1001035 (2010) \\
       - Lu, Y.X. and Xu, W.H., Journal of Proteome Research, Proteomic and phosphoproteomic analysis at diapause initiation in the cotton bollworm, Helicoverpa armigera (2010) \\
       - A Zahiri, K Heimel, R Wahl, M Rath, J Kämper, Am Phytopath Society, e-Xtra (2010) \\

b2gfar_test

2009-04-23T20:43:15+02:00

@@ -19,13 +19,13 @@
  			echo "<strong>Name: ".$rowEmp['name']."</strong><br>";
  		   	echo "Taxa-ID: ".$rowEmp['taxaid']."<br>";
  			echo "Taxa Linage: ".$rowEmp['taxalinage']."<br>";
  			echo "Group: ".$rowEmp['groupid']."<br>";
- 			echo "==== Number of sequences: ".$rowEmp['seqnr']."====";
+ 			echo "Number of sequences: ".$rowEmp['seqnr']."<br>";
  			echo "  ".$rowEmp['annotFileSize']."<br>";
  			echo "b: ".$rowEmp['annotFileZipSize']."<br>";
  			echo "c: ".$rowEmp['goslimFileSize']."<br>";
  			echo "d: ".$rowEmp['goslimFileZipSize']."<br><br>";
  		}
  	}
  }
  </php>

cloud

2009-06-09T16:04:40+02:00

@@ -1 +1,3 @@
  ==== Cloud ====
+ 
+ ~~CLOUD:15~~

cmap_gsea_goetzscore

2009-04-02T12:05:07+02:00

@@ -26,9 +26,9 @@
    * Heat Map Visualisation
    * GoetzScore as functional similarity measurements
  
  ==== Data ====
- [[farmaLists.tar.gz]]
+ {{farmaLists.tar.gz}}
  
  
  ==== Questions (later: Results) ==== 
    * Quality of c-map expression data?

contact

2009-08-05T14:20:43+02:00

@@ -26,9 +26,9 @@
  
  \\
  
  ;-) **Ana Conesa** - aconesa(a)cipf.es - [[http://bioinfo.cipf.es/aconesa|WWW]]  \\ 
- 8-) **Stefan Goetz** - sgoetz(a)cipf.es - {{:cv_stefan_goetz.pdf|CV}}
+ 8-) **Stefan Goetz** - sgoetz(a)cipf.es - {{http://bioinfo.cipf.es/stegotz/cv_stefan_goetz.pdf|CV}}
  
  Bioinformatics Department\\ Centro de Investigación Príncipe Felipe (CIPF)\\ C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanográfico)\\ 46013 Valencia, Spain\\ Tel: +34 963289680 Ext. 1021\\ Fax: +34 963289574\\ http://bioinfo.cipf.es

downloads

2010-07-13T17:19:43+02:00

@@ -3,7 +3,7 @@
    * Run Blast2GO by Java Web Start **([[start_blast2go|here]])**
-   * Documentation and Quick-Start tutorial for an easy start-up with Blast2GO: {{:b2g_tutorial_23062009.pdf|PDF}}
-   * Installation manual on how to set up a local Blast2GO database: [[localgodb|here]] and {{local_b2g_db_tutorial_0709.zip|ZIP}} 
+   * Documentation and Quick-Start tutorial for an easy start-up with Blast2GO: {{:b2g_tutorial_23062009.pdf|PDF}}\\
+   * Installation manual on how to set up a local Blast2GO database: **[[localgodb|here]]**\\
    * Install a local www-BLAST server: [[wwwblast|click here]]
    * Mini-Tutorial on how to prepare and blast locally a GO fasta database for further import into Blast2GO: [[tut| here]]
    * B2G4PIPE - A version for B2G annotation without FrontEnd (GUI) for Pipeline Integration
      * Version 2.3.4: {{:b2gpipe234.zip|WIN}} and {{:b2gpipe234.tar.gz|LINUX}}
@@ -12,9 +12,10 @@
  
  \\
  \\
  \\
+ 
  ==== Script provided by Blast2GO users for Blast2GO users ====
  These scripts are provided as-is. Please contact the respective authors for more information/feedback.
  
    * split and translate big blast output (**txt** formated) into several files in **xml** format: {{:blast2xml.zip|blast2xml.zip}} Author: Laurent Marc
    * split big blast output (xml formated) into severals files: {{:splitxmlblast.zip|splitxmlblast.zip}} Author: Laurent Marc

evaluation

2010-06-07T11:45:50+02:00

@@ -1,5 +1,5 @@
- ====== Evaluation of Blast2GO VALUATION OF BLAST2GO ======
+ ====== Evaluation of Blast2GO ======
  
  ===== Summary =====
  
  Blast2GO (B2G) is a tool designed to enable Gene Ontology (GO) based

faq

2010-08-30T18:30:07+02:00

@@ -13,21 +13,21 @@
  However if you are continuing to have problems then another thing we can do is  to make sure that the network port is actually open from *your* computer.  Not open as per what someone such as your network person says should be.  Not open from looking at someone else's computer.  But rather from *your* computer.  (Story below).  To do this we will use the 'telnet' program in order to side-step any problems that might be due to B2Go.  'Telnet' usually goes to port 23 but most versions of it  can also go to other ports and specifically port 3306 which is the one that the B2Go server uses for annotation.   Unfortunately telnet does vary a bit from operating system to operating system so you may need to change the instructions below.  They did work from WinXP, MacOS 10.4 and Ubuntu 10.  The following is from my Mac.\\
  
  Get to the command line and type in the program, address and the port like so:\\
  \\
- telnet   193.144.127.204   3306 \\
+ //telnet   193.144.127.204   3306// \\
  \\
  You should see something like:
  \\
- Trying 193.144.127.204... \\
- Connected to 193.144.127.204. \\
- Escape character is '^]'. \\
- G \\
- 5.0.32-Debian_7etch12-log?`o:U!AcN=',K#kr}=Vws_aG \\
+ //Trying 193.144.127.204...// \\
+ //Connected to 193.144.127.204.// \\
+ //Escape character is '^]'.// \\
+ //G// \\
+ //5.0.32-Debian_7etch12-log?`o:U!AcN=',K#kr}=Vws_aG// \\
  \\
  The key point to look for is that '5.0.32-Debian' portion of the line.     If you get that then you have connected to the B2Go data base.  The connection should time out and you'll will get something like:\\
  \\
- Connection closed by foreign host.\\
+ //Connection closed by foreign host//.\\
  \\
  But that is fine.  Just get that 'Debian' response. \\
  \\
  If you do not get the response -- especially if you do at least two attempts at least 24 hours apart --  then you have some sort of network problem.  Something somewhere is blocking your network.   Solving this may take quite a bit of effort.  However getting your network guru involved will help.\\

googlegrouppage

2009-10-02T11:34:22+02:00

@@ -1 +1,2 @@
+ ===== Latest 50 Blast2GO Google Group Messages =====
  {{rss>http://groups.google.com/group/blast2go/feed/rss_v2_0_msgs.xml?num=50 50 date 1h}}

home

2010-09-08T16:03:47+02:00

@@ -1,9 +1,9 @@
  ~~META:
  title=Blast2GO
  ~~
  
- <html><p align="center"><span style="color:red;font-size:160%";><a href="http://bioinfo.cipf.es/blast2gocourse">New 2010 courses!</a></span></p></html>
+ <html><p align="center"><a href="http://bioinfo.cipf.es/blast2gocourse"><span style="color:red;font-size:160%";>New 2010 courses!</span></a></p></html>
  
  
  ====== Welcome to Blast2GO ======

info

2008-06-24T15:22:43+02:00

@@ -1 +1 @@
- [[http://www.blast2go.es|{{ :b2gweblogomini.jpg?60 |}}]] 
+ [[http://www.blast2go.org|{{ :b2gweblogomini.jpg?60 |}}]]

licence

2010-06-23T13:54:18+02:00

@@ -5,9 +5,9 @@
  Although best efforts are always applied when developing Blast2GO and related products, we make no warrant nor assumes any legal responsibility for anything related to the Blast2GO project.
  
  === License agreement ===
  
- Copyright is hold by its respective owners but license is hereby granted and therefore **freely available** for all Blast2GO and related resources for personal, academic, and non-profit use. Commercial users should contact us for an individual licence agreement. 
+ Copyright is hold by its respective owners but license is hereby granted and therefore **freely available** for all Blast2GO and related resources. <html><!-- for personal, academic, and non-profit use. Commercial users should contact us for an individual licence agreement. --></html>
  
  === Third Party Licences used by Blast2GO ===
  
    - Apache Project Library's like Batik, Xalan, Jakarta, and many more with Apache License

license

2008-06-20T20:02:13+02:00

@@ -1 +1,2 @@
+ ====== License ======

links

2009-06-09T16:45:48+02:00

@@ -1,34 +1,20 @@
  ====== Interesting Links ======
  
-   * [[afp_go_tools|Comparison of Gene Ontology(GO) Tools for Automatic Function Prediction(AFP)]]
- 
-   * **[[cipf|INTRANET]]**
- 
- 
- we just changes websites - this links will be avalible soon 
  
+ ----
    * [[http://www.geneontology.org/|The Gene Ontology Consortium]]
    * [[http://www.ncbi.nlm.nih.gov/|NCBI - National Center for Biotechnology Information]]
    * [[http://www.ebi.ac.uk/GOA/|GOA - Gene Ontology Annotation Project by EBI]]
    * [[http://www.ebi.ac.uk/|EBI - European Bioinformatics Institute]]
- 
  ----
- 
-   * CIPF - Centro de Investigación Príncipe Felipe
-   * Bioinformatics Department - CIPF
-   * IVIA - Instituto Valenciano de Investigaciones Agrarias
-   * Centro de Genomica - IVIA
-   * Universidad Politécnica de Valencia (UPV)
-   * ITACA - Instituto de Aplicaciones de las Tecnologias de la Informacion y de las Comunicaciones Avanzadas
-   * BET - Bioingeniería, Electrónica y Telemedicina
-   * IBIME - Informática Biomédica
-   * Graphviz - Graph Visualization Software
-   * AT&T - Labs-Research - Graphviz
- 
- ----
- 
-   * BioJava - An open-source project providing a framework for processing biological data
-   * Batik - A Java technology based toolkit for viewing, generation or manipulationthe of Scalable Vector   * Graphics (SVG)
-   * Adobe SVG Viewer 3.0
-   * Gossip Poster - Biological Profiling of Gene Groups utilizing Gene Ontology A Statistical Framework and Software
+   * [[|CIPF - Centro de Investigación Príncipe Felipe
+   * [[|Bioinformatics Department - CIPF
+   * [[|IVIA - Instituto Valenciano de Investigaciones Agrarias
+   * [[|Centro de Genomica - IVIA
+   * [[|Universidad Politécnica de Valencia (UPV)
+   * [[|ITACA - Instituto de Aplicaciones de las Tecnologias de la Informacion y de las Comunicaciones Avanzadas
+   * [[|BET - Bioingeniería, Electrónica y Telemedicina
+   * [[|IBIME - Informática Biomédica
+   * [[|Graphviz - Graph Visualization Software
+   * [[|AT&T - Labs-Research - Graphviz

localgodb

2010-07-13T17:55:47+02:00

@@ -1,7 +1,7 @@
  ===== Local Blast2GO Database Installation =====
    * Version 3 - 01.07.2009
-   * **Download:** {{local_b2g_db_tutorial_0709.zip|ZIP}} 
+   * **Download:** {{:local_b2g_db_tutorial_0809.tar.gz|tar.gz}}, {{:local_b2g_db_tutorial_0809.zip|zip}}
  
  
  ==== Introduction ====
  This page describes how to create a local installation of the B2G MySQL database and is intended for users with some basic knowledge in MySQL databases and general server administration tasks. If you are not able to follow the steps given here, we recommend you to ask for some help from your system administrator.

map

2009-06-25T18:41:31+02:00

@@ -1,6 +1,6 @@
  ====== World map of Blast2GO usage ======
-   * Blast2GO usage during the last 24 hours. \\ Images are generated at 6h,12h,18h and 24h CET.
+   * Blast2GO access during the last 24 hours. Images are updated every hour.
  [[http://www.blast2go.org/_media/b2g_usage_4096.jpg?direct&nocache|{{http://www.blast2go.org/_media/b2g_usage_1024.jpg?700&direct&nocache|Usage during the last day (last 24 hours)}}]]
  
   <html><!--   * Usage during the last week
  [[http://bioinfo.cipf.es/access_map/blast2go/tool_usage_604800.jpeg?nocache&direct|{{http://bioinfo.cipf.es/access_map/blast2go/thumb_86400.jpeg?700&direct&nocache|Usage during the last week}}]]--></html>

method

2009-06-09T16:47:16+02:00

@@ -14,4 +14,8 @@
  
  {{ :b2gpipeline.jpeg?500&direct |}}
  
  Application overview: The figure shows schematically a typical run of B2G. Used symbols are described in the embedded legend. Numbered circles denote the major application steps. From the left to the right these are (1) Blasting: a group of selected sequences is blasted against either the NCBI or custom databases, (2) Mapping: GO terms are mapped on the blast results using annotation files provided by the GO Consortium that are downloaded on a monthly basis at the Blast2GO server, (3) Annotation: sequences are annotated using an annotation rule that takes parameters provided by the user, (4) Statistical analysis: optionally, analysis of GO term distribution differences between groups of sequences can be performed and (5) Visualization: annotation and statistics results can be visualized on the GO DAG. At each of these steps, different charts are available to evaluate the progress of the analysis and data can be saved and exported in different formats.
+ 
+ ====Comparison of Gene Ontology(GO) Tools for Automatic Function Prediction====
+ 
+   * [[afp_go_tools|Comparison of Gene Ontology(GO) Tools for Automatic Function Prediction(AFP)]]

nespresso

2009-02-24T12:54:38+02:00

@@ -1,4 +1,11 @@
+ 
+ ===Next Order===
+ ^Cafetero^Ristretto^Apreggio^Roma^Vivalto^Livanto^
+ |nombre|0|0|0|0|0|
+ 
+ 
+ ===Febrero===
  ^Cafetero^Ristretto^Apreggio^Roma^Vivalto^Livanto^
  |Stefania|10|10|20|0|0|
  |PabloM|20|10|0|20|0|	
  |Marc|50|0|0|0|0|

newfeatures

2010-07-30T13:38:33+02:00

@@ -1,8 +1,11 @@
  ====== Vote for new features ======
  
  With this new section we would like to invite you to directly contribute to the future developments of Blast2GO. Here you can propose and vote functionalities which will be considered in future developments of Blast2GO. Your suggestions and opinions will help us to prioritize the software development process based on the concepts of a [[http://en.wikipedia.org/wiki/Feature_Driven_Development|Feature Driven Development]]. 
  If you want to suggest a new feature which you think could be useful for you and the other Blast2GO users please go to **[[http://blast2go.uservoice.com|blast2go.uservoice.com]]** and directly add your idea to this list. After some time we can see on this page if other user agree and would like to see your idea implemented in Blast2GO.
+ 
+ Thank you very much for your contribution, feedback and suggestions!!
+ 
  <html><!--
  [[http://blast2go.uservoice.com|{{:uservoice.gif|}}]]
  
  [[https://blast2go.uservoice.com/forums/66021-general/activity.atom|]] **Latest suggestions and feedbacks - click to VOTE NOW...**

news

2009-01-09T12:12:14+02:00

@@ -71,11 +71,11 @@
  A tutorial to set up a local B2G database is now available at Downloads.
  
  :-o 01.10.2005 - //Stefan Goetz// \\
  Meeting Photo: 2005 GO Users Meeting \\
- {{:photo_go_user.jpg?100&direct | 2005 GO Users Meeting}}\\ \\ \\ \\
+ {{:photo_go_user.jpg?100&direct | 2005 GO Users Meeting}}\\ \\ \\
  
  :-o 18.09.2005 - //Stefan Goetz// \\
  New Blast2GO Mail List!
  To support the use of B2G and to keep you up to date we have created a mail group to share the information. Feedback, support, discussion, news, announcements, comments, suggestions and bug-reports can be posted here.
  You are invited to join at http://groups.google.com/group/Blast2GO
  Thanks in advanced for your future contributions.

screenshots

2008-06-26T16:50:15+02:00

@@ -1,19 +1,19 @@
  ====== Screenshots ======
    * Blast your sequences against a local BLAST server or through the NCBI.\\ 
- {{ :screenshots:blasting.jpg?300 |}}\\ 
+ {{ :screenshots:blasting.jpg?300&direct |}}\\ 
  
    * Link the retrieved homologues to the functional annotation provided by the Gene Ontology Consortium.\\ 
  {{ :screenshots:mapping.jpg?300 |}}\\ 
  
    * Apply the Blast2GO annotation rule to the dataset.\\ 
- {{ :screenshots:annotation.jpg?300 |}}\\ 
+ {{ :screenshots:annotation.jpg?300&direct |}}\\ 
  
    * Visually review single annotations.\\ 
- {{ :screenshots:singlesequencegraph.jpg?300 |}}\\
+ {{ :screenshots:singlesequencegraph.jpg?300&direct |}}\\
  
    * Check the biological background of a whole dataset using "Combined Graphs".\\ 
- {{ :screenshots:combinedgraph.jpg?300 |}}\\ 
+ {{ :screenshots:combinedgraph.jpg?300&direct |}}\\ 
  
    * Perform a functional enrichment study comparing to list of annotated genes/proteins\\ 
- {{ :screenshots:fisher.jpg?300 |}}\\ 
+ {{ :screenshots:fisher.jpg?300&direct |}}\\

sidebar

2010-08-27T11:23:18+02:00

@@ -21,13 +21,13 @@
  \\
  [[ newfeatures |{{ :uservoice.gif?100 |}}]]
  ------
  [[http://twitter.com/blast2go|{{:twitter_feed_icon.png|}}]][[http://twitter.com/statuses/user_timeline/74696035.rss|{{:rss.png|}}]] **TWITTER NEWS**
- {{rss>http://twitter.com/statuses/user_timeline/74696035.rss 5 date 5h}}
+ {{rss>http://twitter.com/statuses/user_timeline/74696035.rss 5 date 12h}}
  
  ------
  
  [[http://groups.google.es/group/Blast2GO|{{:googlegroupicon.jpg?20|}}]][[http://groups.google.com/group/blast2go/feed/rss_v2_0_topics.xml|{{:rss.png|}}]] **GOOGLE GROUP Discussion**
- {{rss>http://groups.google.com/group/blast2go/feed/rss_v2_0_topics.xml 5 date 1h}}
+ {{rss>http://groups.google.com/group/blast2go/feed/rss_v2_0_topics.xml 5 date 12h}}
  [[googlegrouppage|... more messages]]

simap

2008-06-24T20:41:20+02:00

@@ -1,4 +1,4 @@
  ===== SIMAP - The Similarity Matrix of Proteins =====
- SIMAP is a database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes.\\
+ SIMAP is a database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes.\\ \\
  [[http://webclu.bio.wzw.tum.de/portal/web/simap/|Link to Simap]]

simap2go

2008-06-27T15:52:05+02:00

@@ -1,2 +1,3 @@
  ===== Simap2GO =====
+ ...coming soon

species

2008-06-20T20:02:13+02:00

@@ -1 +1,14 @@
- 
+ ==== /home/sgoetz/Desktop/7955_danio.annot ====
+ === General Information ===
+ 166 Sequences annotated by Blast2GO.\\ 
+ === Images ===
+   * annotStat.png
+ {{ :/home/sgoetz/Desktop/7955_danio.annot_annotStat.png?300 |}}\\ 
+   * levelStat.png
+ {{ :/home/sgoetz/Desktop/7955_danio.annot_levelStat.png?300 |}}\\ 
+   * goCountMf.png
+ {{ :/home/sgoetz/Desktop/7955_danio.annot_goCountMf.png?300 |}}\\ 
+   * goCountBp.png
+ {{ :/home/sgoetz/Desktop/7955_danio.annot_goCountBp.png?300 |}}\\ 
+   * goCountCc.png
+ {{ :/home/sgoetz/Desktop/7955_danio.annot_goCountCc.png?300 |}}\\

speedtest

2009-01-20T16:41:26+02:00

@@ -8,13 +8,13 @@
  Speed Test requires at least version 8 of Flash. <a href="http://www.macromedia.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash">Ple
  ase update your client</a>.
  </div>
  <script type="text/javascript">
-    var so = new SWFObject("speedtest.swf?v=2.0.7", "speedtest", "450", "250", "8", "#171715");
+    var so = new SWFObject("mini/speedtest.swf?v=2.0.7", "speedtest", "450", "250", "8", "#171715");
     so.addVariable("upload_extension", "php");
     so.write("speedtest");
  </script>
  <!-- END SPEED TEST - DO NOT ALTER ABOVE -->
  
  </td></tr>
  </table>
  </html>

start

2008-05-09T16:28:43+02:00

@@ -1,13 +1,13 @@
  ====== Start Blast2GO by Java Web Start ======
  
- ===== **IMPORTANT NOTE: =====
+ ==== IMPORTANT NOTE: ====
  
  The minimum requirements to run Blast2GO are a working Java installation (version > 1.5) (on Win,Linux,Mac etc.) In case you do not, get the actual Java Runtime Environment (JRE) from http://java.sun.com.
  
- To connect to the B2G database you (your computer settings, your personal firewall) and your institute (institutes firewall, providers network settings) has to permit outgoing tcp connections on port 3306. Normally outgoing connections of this type are always permitted unless you have a highly restrictive network policy. (To easily test if B2G works fine press one of the green arrows in the B2G main frame, some GO graphs should appear more or less instantly. The most actual DB is called b2g_apr (b2g_nov) and the host's IP is: 193.144.127.204
+ To connect to the B2G database you (your computer settings, your personal firewall) and your institute (institutes firewall, providers network settings) has to permit outgoing tcp connections on port 3306. Normally outgoing connections of this type are always permitted unless you have a highly restrictive network policy. (To easily test if B2G works fine press one of the green arrows in the B2G main frame, some GO graphs should appear more or less instantly. The most actual DB is called **b2g_apr** (b2g_nov) and the host's IP is: **193.144.127.204**
  
- Usefull commands for Linux users:
+ __Usefull commands for Linux users:__
  - check Java: "java -version"
  - check/find Java Web Start: "whereis javaws"
  - Run Java Web Start: "javaws -viewer" (in the Java Control Panel, under "Advanced", set console to "show console")
  - Start B2G from command line: "javaws http://blast2go.bioinfo.cipf.es/webstart/blast2go_cipf.jnlp"
@@ -18,4 +18,6 @@
  
  ^ Please select: ^^^^
  | 256 MB | 512 MB | 1024 MB | 2048 MB |
  | very small projects | default | > 10000 seqs | > 20000 seqs |
+ 
+

start_blast2go

2010-06-08T16:07:30+02:00

@@ -5,9 +5,9 @@
  ===== Java =====
  **INSTALL JAVA:**\\
  The minimum requirement to run Blast2GO is a working Java installation (version > 1.5) (on Win,Linux,Mac etc.) In case you do not have that already please install the actual Java Runtime Environment (JRE) from http://www.java.com/download
  
- **JAVA WEB SATRT** \\
+ **JAVA WEB START** \\
  By Java Web Start technology (which is included in JAVA) you will be provided with 
  the latest Blast2GO update each time you start the application. 
  If your browser hasn't been set up to run Java WebStart JNLP
  files, the link above will download a file called

supplementary

2008-08-03T19:31:29+02:00

@@ -1,7 +1,6 @@
  ====== Supplementary Material ======
  **High throughput functional annotation and data mining with the Blast2GO suite** \\
- [[afp_go_tools]]
  last update 22.08.2008 \\ \\ 
    * Annotation performance comparision: {{:suppl_annot_perf.xls|suppl_annot_perf.xls}}
    * Functional genomics study: {{:suppl_funct_genom.xls|suppl_funct_genom.xls}}
    * Mannual curation results: {{:suppl_man_curation.xls|suppl_man_curation.xls}}

survey

2010-06-14T14:59:53+02:00

@@ -33,4 +33,28 @@
  * Public research institute
  * Private research institute
  * Other
  </vote>
+ 
+ <vote Profile2 check=ip>
+ I'm a:
+ * Student
+ * Pre-Doc
+ * Researcher
+ * IT-related
+ * Principal Investigator
+ * Other
+ </vote>
+ 
+ <vote Profile3 check=ip>
+ I'm a:
+ * (Molecular) Biologist
+ * Biochemist
+ * Bioinformatician
+ * Computer Scientist
+ * Statistician/Mathematician/Physician
+ * Biotechnologist
+ * Pharmacologist
+ * A little bit of everything
+ * None of the above
+ </vote>
+

template

2008-06-25T18:37:54+02:00

@@ -19,9 +19,9 @@
  {{ speciesDist_rhesus.png?500 |speciesDist}}  
  {{ length_seq_rhesus.png?500 |length_seq}}       
  
  ==== Mapping Results ====
- Sequences without Gene Ontologies terms: 38.143
+ Sequences without Gene Ontologies terms: 38.143\\
  {{ ECDist_rhesus.png?300 |Evidence code distribution for sequences}}
  {{ EC_dist_hit_rhesus.png?300 |Evidence code distribution for hits}}
  {{ database_sources_rhesus.png?500 |Database distribution}}

termsofuse

2009-03-17T15:27:03+02:00

@@ -1 +1,27 @@
+ ===== Terms of Use =====
+ 
+ === Disclaimer ===
+ 
+ Although best efforts are always applied when developing Blast2GO and related products, we make no warrant nor assumes any legal responsibility for anything related to the Blast2GO project.
+ 
+ === License agreement ===
+ 
+ Copyright is hold by its respective owners but license is hereby granted and therefore **freely available** for all Blast2GO and related resources for personal, academic, and non-profit use. Commercial users should contact us for an individual licence agreement if necessary. 
+ 
+ === Third Party Licences used by Blast2GO ===
+ 
+   - Apache Project Library's like Batik, Xalan, Jakarta, and many more with Apache License
+   - JFree with GNU Lesser General Public License
+   - BioJava with GNU Lesser General Public License
+   - GraphViz - Graph Visualization Software with Common Public License
+   - MySQL Connector/J wiyh MySQL Open Source License (GPL) or MySQL Commercial License (see MySql Licence Policy)
+   - Gossip MicroDiscovery GmbH Software License Agreement
+   - GO-Slim and BioPerl: Perl Artistic License
+   - Kegg DB and API: academic use is free, non-academic users need a licencse from Pathway Solutions
+   - Interpro (free to all public under certain conditions)
+   - Annex (not defined)
+   - Gene Ontology (free to all public under certain conditions)
+ 
+ === Imprint ===
+ All logos and trademarks in this site are property of their respective owner. Blast2GO has no influence on the design and contents of third party internet web sites. Blast2GO therefore expressly distances itself from the material of all third party internet web sites, even if the Blast2GO web site links to these external sites. The declaration is valid for all links given on our web site and the material of all sites reached via banners and links on the Blast2GO web site.

test

2009-08-04T13:23:44+02:00

@@ -1,2 +1,33 @@
  
+ <vote Usage check=ip>
+ The Blast2GO feature I use most frequently is:
+ * Just BLASTing
+ * GO functional annotation
+ * InterPro and KEGG annotation
+ * Graph Visualisation
+ * Enrichment analysis
+ * GO-Slim feature
+ * Transform/Filter/Import/Export annotations
+ * A bit of everything
+ </vote>
  
+ <vote Research check=ip>
+ The research I'm doing is related most to:
+ * Transcriptomics
+ * Whole-genome characterization
+ * Expressed Sequence Tags
+ * Next-generation sequencing
+ * Comparative genomics
+ * Proteomics
+ * Systems biology
+ * Protein-protein interactions
+ * Functional genomics in general
+ </vote>
+ 
+ <vote Profile check=ip>
+ I'm from a:
+ * University
+ * Private company
+ * Public research institute
+ * Private research institute
+ </vote>

tut

2010-01-07T13:45:09+02:00

@@ -1,5 +1,5 @@
- ===== Format, blast a fasta-file and import results to Blast2GO =====
+ ===== Format and blast a fasta-file and import results into Blast2GO =====
  
  Tips to format a database so that the results can than later be imported to blast2go without problems. The important thing here is to adapt the fasta sequence descriptions in a way that they can be parsed without problems. additionlly you will have to run "formatdb" with the "-o T" and ·-a F" option. 
  
  **1.** Download a fasta file of your choice and unzip it.

wwwblast

2009-09-18T17:38:49+02:00

@@ -23,6 +23,6 @@
  
  Good luck! \\
  (author: Stefan Götz)
  
- PD: Another tutorial on how to set up a www-blast server can be found here: 
+ PD: Another tutorial on how to set up a www-blast server can be found here: \\
  http://blog.pansapiens.com/2008/08/25/setting-up-wwwblast-on-ubuntu-apache/

A universal Gene Ontology annotation, visualization and analysis tool for functional genomics research