When Biomedicalit Met Java

Release Notes (2012/05/24)

2012-05-24T17:58:00.001+08:00

VarioWatch

Add information of disease-associated variant from miRdSNP, SNPedia and National Human Genome Research Institute (NHGRI) genome-wide association study (GWAS) catalog data.
Fix bug: Retrieve reference of genes now works normally.
Fix bug of MegaQuery: Variant located within two genes which have the same gene start now can be annotated appropriate.

PrimerZ

Add new species: Cod, Coelacanth, Gibbon, Horse, Kangaroo Rat, Lamprey, Panda, Tasmanian Devil and Turkey.
Update Ensembl database to release 66.

QualiSeq

Update Ensembl sequence to release 67.
Fix bug of query by taskID: Retrieve results using url link of taskID now works correctly.

Release Notes(2012/04/16)

2012-04-16T12:12:00.000+08:00

Fix bugs of VarioWatch and QualiSeq: query by a batch of variations and gene.

Release Notes (2012/04/09)

2012-04-09T18:08:00.001+08:00

VCF format (version 4.x) input supported

MegaQuery Download now supports the annotation of SNP and small indel in Variant Call Format (VCF) version 4.x, with output in CSV format.

Release Notes(2012/02/02)

2012-02-03T15:38:00.001+08:00

Bug fixes: The progress bar shows message of invalid taskID when submitting.

Release Notes(2011/12/30)

2011-12-29T17:57:00.002+08:00

Add link of VarioWatch result in the MegaQuery Download file (variation_annoation.csv).

Release Notes(2011/12/05)

2011-12-05T18:00:00.002+08:00

Add filters of risk level and of location.
Support file format of Illuma CASAVA 1.8.x for MegaQuery download. ('snp.txt' and 'indel.txt' in CASAVA Variant Detection output folder.)
Modify the logic for filtering out variants in 1000 Genomes Project. Variants with the same chromosome and pysical position but different allele as the queries no longer appear in 1000genome_allele_freq.csv.
Modify format of 1000genome_allele_freq.csv file. Replace field "Query Name" by two fields "Chr" and "Position".

Release Notes(2011/11/07)

2011-11-07T16:51:00.002+08:00

Update data of 1000 Genomes Project to October 2011 Integrated Variant Set of for VarioWatch (Build NCBI 37.2).

Release Notes(2011/10/25)

2011-10-25T16:52:00.002+08:00

1. Add filter for MegaQuery Download.
2. Add data release on June 23, 2011 of 1000 Genomes Project for VarioWatch (Build NCBI 37.2).

Release Notes(2011/10/07)

2011-10-07T17:28:00.003+08:00

1. Update dbSNP version from dbSNP132 to dbSNP134 for GenePipe NCBI 37.2.
2. Update Ensembl version from release 63 to release 64.
3. QualiSeq batch download supports FANS format.
4. QualiSeq bugs fix:

Sequence download.
SNP Info of UCSC and of Ensembl.

5. MegaQuery performance improvement.
6. MegaQuery Indel Variations:

Add location type of "GT-AG splice site".
Add new info: "Risk by Location".
Add ESE/ESS motif analysis.

Release Notes(2011/09/26)

2011-09-26T17:01:00.001+08:00

MegaQuery Download:
1. Improve location type.

add Intragenic location for indel variation.
add Intragenic location and GT-AG splice site for single point variation.

2. Improve gene symbol for variations in intragenic region.
3. Add risk type and risk level for single point variation in GT-AG splice site.
4. Add 1000 Genomes data for single point variation(NCBI36 only).

Release Notes(2011/09/08)

2011-09-08T16:38:00.001+08:00

MegaQuery Download supports indel type variations.
MegaQuery Download provides gene annotation file.

Release Notes(2011/08/18)

2011-08-18T14:58:00.003+08:00

MegaQuery Download is now available for VarioWatch NCBI36 version.

Release Notes(2011/08/08)

2011-08-11T10:58:00.001+08:00

QualiSeq: update Ensembl human genome sequence to release 63.
PrimerZ: update Ensembl database to release 63.
Variowatch bug fix: motif sequence of ESE and ESS mapping to target sequence on reverse strand displayed incorrectly from 3 prime end to 5 prime end.
New function of Variowatch: fast download of annotations for millions of variants.

Release Notes(2011/07/01)

2011-07-01T11:12:00.001+08:00

We have changed web domain from "http://genepipe.ngc.sinica.edu.tw" to "http://genepipe.ncgm.sinica.edu.tw"

Release Notes(2011/06/23)

2011-06-24T09:59:00.002+08:00

1.VarioWatch has been updated to human genome NCBI Build 37.2
2.Update database of PrimerZ to NCBI Build 37.2

Release Notes (2011/04/26)

2011-04-26T16:57:00.004+08:00

VarioWatch has been updated to a beta version based on human genome NCBI Build 37.1
Update database of PrimerZ to Ensembl Release 62 and NCBI Build 37.1
Fix SeqTool SNP extraction problem with older dbSNP version (131).

Release Notes (2011/03/08)

2011-03-08T17:30:00.001+08:00

1. Update human genome sequence from Ensembl to release 61 of the QualiSeq.
2. Update database of PrimerZ to Ensembl Release 61.
3. Upgrade human genome assembly version to NCBI 37.2 and dbSNP to version 132 of VisualSNP
4. Upgrade human genome assembly version to NCBI 37.2 and fix the analysis of mouse variats query of FANS

Holiday Wishes from GenePipe Team

2010-12-23T11:13:00.003+08:00

GenePipe Team Wishes You Merry Christmas and Happy New Year 2011!

Release Notes(2010/11/25)

2010-11-26T14:11:00.003+08:00

Update human genome sequence from Ensembl to release 60 of the QualiSeq.
Update allele frequency data from 1000 Genomes to release 2010/10 of the Variowatch.
Update Pathway data from KEGG of the Variowatch.
Update Gene ontology data of the Variowatch.
Update Unists data of the Variowatch.
Update UniProt data of the Variowatch.

Release Notes(2010/11/01)

2010-11-02T10:31:00.000+08:00

Fix data collection modules for NCBI dbSNP 132 and NCBI gene of VisualSNP and FANS.
Update human genome sequence from Ensembl to release 59 of QualiSeq.

Release Notes(2010/09/20)

2010-09-21T10:16:00.000+08:00

Add faster download (without the PutMed Reference) by Variowatch

Remove NGC Super Control (Han Chinese) affy 500K data in the population diversity

Release Notes(2010/09/06)

2010-09-06T17:25:00.001+08:00

1.Update Ensembl data to v59.
2.Update Journal Reference.
3.Fix Fans, VisualSNP and QualiSeq bug.
4.Update Hapmap data (Allele frequencies 2010/08_phaseII+III)
5.Fix PrimerZ config file

Release Notes(2010/08/02)

2010-07-30T10:00:00.005+08:00

Variowatch

add 1000 genome pilot 1 frequencies in the non-coding.
fix SNPs query type.
allele frequency data of variations are avaliable to download.

Release Notes(2010/07/21)

2010-07-20T15:10:00.001+08:00

Variowatch

add 1000 genome pilot 3 allele frequencies.

Release Notes(2010/07/08)

2010-07-08T11:00:00.004+08:00

Variowatch

update analysis database.
Sequence query bug fixed.
add 1000 genome pilot 1 allele frequencies.

PrimerZ

upload parameters user interface modify
Query type of gene mask function fixed