Release VB-2016-04

We are pleased to announce the April 2016 release of VectorBase (VB-2016-04):

• New organism Cimex lectularius (Harlan strain)
• New Aedes aegypti gene expression profiling data for three flavivirus infection time courses (Dengue, West Nile and Yellow Fever viruses)
• New mass spectrometry data for Anopheles gambiae and Ixodes scapularis
• Updated InterPro domain annotation of all VectorBase genomes
• InterPro domain annotation of all transcriptome assemblies
• New date search in the PopBio map
• A single nucleotide polymorphism (SNP) calling workflow added to Galaxy
• New password expiry requirements
• We have restructured and greatly improved the "About" page. It is design to give current and new users a quick guide of what can be done with the site, including some sample queries with analyses, and much more
• The "Search" tutorial has been updated, the material includes practice exercises with answer key, and new video with its slides
• We now have a YouTube Channel were we will add video tutorials. This time we invite you to watch "Tour", which is a (6 min) overview of the site navigation, data types, tools and resources

New password expiry requirements

VectorBase users who have an account will be required to update the password every six months. Thirty (30) days before that an email will be sent to account holders to create a new password, the email will have the necessary links and instructions. You do not need to update your Web Apollo password, this is a separate account.

Genomes

Released genomes, with gene predictions

Organism	Strain	Assembly	Gene set	Gene Count	Browser
Aedes aegypti	Liverpool	AaegL3	AaegL3.3	17 478
Aedes albopictus	Foshan	AaloF1	AaloF1.1	17 592
Anopheles albimanus	STECLA	AalbS1	AalbS1.3	12 509
Anopheles arabiensis	Dongola	AaraD1	AaraD1.3	13 849
Anopheles atroparvus	EBRO	AatrE1	AatrE1.3	14 244
Anopheles christyi	ACHKN1017	AchrA1	AchrA1.3	11 162
Anopheles coluzzii	Mali-NIH	AcolM1	AcolM1.2	14 711
Anopheles culicifacies A	A-37	AculA1	AculA1.3	14 889
Anopheles darlingi	Coari	AdarC3	AdarC3.3	10 961
Anopheles dirus	WRAIR2	AdirW1	AdirW1.3	13 299
Anopheles epiroticus	Epiroticus2	AepiE1	AepiE1.3	12 705
Anopheles farauti	FAR1	AfarF2	AfarF2.1	13 462
Anopheles funestus	FUMOZ	AfunF1	AfunF1.3	13 884
Anopheles gambiae	PEST	AgamP4	AgamP4.3	13 793
Anopheles maculatus B	maculatus3	AmacM1	AmacM1.3	15 050
Anopheles melas	CM1001059	AmelC2	AmelC2.1	15 850
Anopheles merus	MAF	AmerM2	AmerM2.1	13 798
Anopheles minimus	MINIMUS1	AminM1	AminM1.3	13 231
Anopheles quadriannulatus A	SANGQUA	AquaS1	AquaS1.3	13 992
Anopheles sinensis	SINENSIS	AsinS2	AsinS2.1	13 331
Anopheles sinensis	China	AsinC2	AsinC2.1	19 815
Anopheles stephensi	SDA-500	AsteS1	AsteS1.3	13 764
Anopheles stephensi	Indian	AsteI2	AsteI2.2	12 350
Biomphalaria glabrata	BB02	BglaB1	BglaB1.3	14 423
Cimex lectularius	Harlan	ClecH1	ClecH1.2	14 085
Culex quinquefasciatus	Johannesburg	CpipJ2	CpipJ2.2	19 363
Glossina austeni	TTRI	GausT1	GausT1.3	20 309
Glossina brevipalpis	IAEA	GbreI1	GbreI1.3	15 032
Glossina fuscipes	IAEA	GfusI1	GfusI1.3	20 737
Glossina morsitans	Yale	GmorY1	GmorY1.5	13 034
Glossina pallidipes	IAEA	GpalI1	GpalI1.3	19 852
Glossina palpalis	IAEA	GpapI1	GpapI1.1	20 726
Ixodes scapularis	Wikel	IscaW1	IscaW1.4	20 771
Lutzomyia longipalpis	Jacobina	LlonJ1	LlonJ1.2	10 494
Musca domestica	Aabys	MdomA1	MdomA1.1	15 803
Pediculus humanus	USDA	PhumU2	PhumU2.1	11 699
Phlebotomus papatasi	Israel	PpapI1	PpapI1.2	12 685
Rhodnius prolixus	CDC	RproC3	RproC3.1	16 843
Sarcoptes scabiei var. canis	Arlian	SscaA1	SscaA1.1	10 679
Stomoxys calcitrans	USDA	ScalU1	ScalU1.1	16 636

In this release we have added the Harlan strain of Cimex lectularius (the bed bug). Protein features for all species have been updated, using InterPro version 55.0.

Expression data

In this release we have added a new experiment profiling gene expression in response to several different flavivirus infections.

Population Biology/Insecticide Resistance

Four insecticide resistance papers have been added:

• Fonseca-González, I., Quiñones, ML., Lenhart, A., Brogdon WG (2011) Insecticide resistance status of Aedes aegypti (L.) from Colombia
• Hammad, M., Ahmed, N., Khan, IA., Shah, B. Kan, A., Ali, M., Rasheed, MT., Junaid, K., Adnan, M., Zaki, AB., Ahmed, S (2015) Studies on the efficacy of selected insecticides against Anopheles mosquitoes of village Goth Bhoorji (Sindh) Pakistan
• Ocampo, CB., Salazar-Terreros, MJ., Mina, NJ., McAllister, J., Brogdon W (2012) Insecticide resistance status of Aedes aegypti in 10 localities in Colombia
• Sahu, SS., Gunasekaran, K., Vijayakumar, T., Jambulingam P (2015) Triple insecticide resistance in Anopheles culicifacies: a practical impediment for malaria control in Odisha State, India

These are all available in the PopBio map which now has newly added date and normalized insecticide resistance value search functionality.

Variation Data

Summary of available variation data by organism

No variation updates have been performed this release.

Tutorials

Follow this link for all the site tutorials, which includes material such as videos with its slides, practice exercises with answer keys, and sample files. Visit our new YouTube Channel to watch all our video tutorials, we plan to add one for each release. The video slides (including demo outlines), are in our regular tutorial pages. The new and updated tutorials for this release are:

• Tour and
• Search

Future releases

The next VectorBase release (VB-2016-06) is scheduled for late June.

Other known issues

• The tools for the Variation Effect Predictor (VEP) and gene id updates are currently unavailable. We are working to correct this, and will update the release notes as soon as the tools can be used.
• The PopBio map has a new seasonal search facility. However, please note that this is not yet working to our full satisfaction, and consider this as a "beta" feature. We plan to announce a fully working version in the next release.

Please report any problems to the helpdesk.