Here is a collection of links to assist researchers in their work. We understand that tools and databases are frequently updated, so please get in touch to let us know what is missing!
This page is part of the redeveloped resources section on the Node, you can find out more about the update here.
Species resources and databases
Databases of species spanning a wide range of model organisms including vertebrates, invertebrates and plants as well as organ systems, genomics and other useful databases.
Tools
List of tools to help with bioinformatics, image analysis and genome editing as well as experimental design.
Travel grants & research tips
List of travel grant applications to allow early-career researchers to attend conferences and workshops as well as to undertake collaborative research (note varying deadlines so be sure to apply several months in advance of planned visits or meetings!). Also features links for undergraduate summer studentships and some collected research tips.
Species resources and databases
Model organisms
Vertebrates
Avian
NARF – the National Avian Research Facility at the University of Edinburgh, which provides resources, collaborative expertise and advice for avian biology research
GEISHA – chick expression data for first six days of development.
Axolotl
Ambystoma Genetic Stock Center (AGSC)
Bovine
Crocodile
Dog
Goat
Human
1000 Genomes – catalogue of human genomic variation.
BrainSpan Atlas – database containing transcriptional data for different developmental stages of the human brain.
HDBR – collection of human embryonic and fetal material ranging from 3 to 20 weeks of development.
HDBR Atlas – human developmental studies network.
HUGO – human gene nomenclature.
Kyoto Human Embryo Visualization Project – database with almost 1300 embryos imaged using an MR microscope or EFIC.
The Virtual Human Embryo – images of embryos presenting all 23 Carnegie stages during the 8-week embryonic period.
Horse
Kangaroo
Medaka
Medaka Expression Pattern Database (MEPD)
MBase – Medaka Genome Database.
Mouse
4D Atlas of mouse development (E11.5 – E14).
EMAGE – database of in situ gene expression data in the mouse embryo.
EMAP – digital atlas of mouse development.
eHistology – Kaufman’s histological sections and annotations.
genepaint – digital atlas of gene expression patterns in the mouse.
IGTC – mouse ES cell gene trap database.
International Mouse Phenotyping Consortium (IMPC)
Mouse Genome Informatics (MGI) – integrated gene expression, phenotype, and gene ontology annotations for mouse genes, as well as complete gene and allele catalogs.
Monkey
Opossum
Pufferfish
Rat
Tiger
Xenopus
European Xenopus Resource Centre
Zebrafish
ZMP – Zebrafish Mutation Project.
Collated databases
AgBase – curated resource for functional analysis of agricultural plant and animal gene products.
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Invertebrates
Ant
Fourmidable – ant genomics database.
Aphid
Bee
Butterfly
Drosophila
Drosophila Network resources – full list of Drosophila resources, curated by FlyBase.
Echinoderm
Hymenoptera
Planarian
Schmidtea mediterranean Genome Database (SmedGD)
Silkworm
Tunicates
Worms
Caenorhabditis Genetics Center (CGC) – stock centre.
WormAtlas – Database of behavioral and structural anatomy of C. elegans.
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Plants
Arabidopsis
The Arabidopsis Information Resource (TAIR)
Cacao
Citrus
Maize
Maize Genetics and Genomic Database (MaizeDB)
Rosaceae
GDR – Genome Database for Rosaceae.
Soy
Collated databases
Gramene – comparative genome analysis of grasses.
TreeGenes – forest tree genome database.
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Other
Chlamydomonas
Dictyostelium
Tetrahymena
Tetrahymena Genome Database Wiki
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Organ Systems
GenitoUrinary Development Molecular Anatomy Project (GUDMAP)
Facebase – craniofacial development and malformation.
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Genomics
ArrayExpress – Archive of Functional Genomics Data.
DDBJ – DNA data bank of Japan.
Ensembl – Eukaryotic genome data.
GenBank – NIH genetic sequence database.
Gramene – resource for comparative plant genomics.
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Others
BioSharing – curated portal ensuring that standards, databases and policies in the life sciences are registered, informative and discoverable.
Monarch Initiative – linking human disease with model organism phenotypes.
NIH 3D Print Exchange – database of scientifically accurate 3D printing models.
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Tools
Bioinformatics toolkits
- BLAST for DNA & protein sequence searching.
- HMMER for searching for sequence homologs and making sequence alignments.
- Clustal Omega to generate alignments between >3 sequences.
- JIGSAW is a downloadable tool to predict gene models.
- GENSCAN predicts exon-intron structures in genomic sequences.
- MEGA allows building of phylogenetic trees.
- EBI– variety of resources from the European Bioinformatics Institute.
- Gene ontology– collaborative effort to address the need for consistent descriptions of gene products across databases.
- NCBI– variety of resources from the National Center for Biotechnology Information.
- Review article containing tables of many useful bioinformatics resources.
- Collection of Read Alignment Software Tools for WGS analysis – BOWTIE is a particularly good short read aligner.
- Rosalind is a useful platform to self-teach bioinformatics and programming with a focus on Python.
- NC3R tool to help optimise experimental design.
- OmniPath: literature curated human signaling pathways
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Genome editing tools
- ECRISP – design of CRISPR constructs.
- E-TALEN– design of TALEN constructs.
- CCTop – CRISPR/Cas9 target online predictor.
- Mojo Hand – CRISPR and TALEN design tool.
- TALengineering – comprehensive resource of information and resources for practising engineered TAL effector technology.
- ZiFiT Targeter – Zinc finger nuclease sites identifier.
- Addgene – global plasmid repository.
- List of genome editing tools from OmicTools.
- Nature review of delivery technologies for genome editing.
- CRISPR fly design
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Imaging tools
- Colour Universal Design – useful advice on how to display microscopy images in a colourblind-friendly way.
- ImageJ/Fiji – open source image processing software with plenty of additional downloadable macros.
- MorphoGraphX – platform for quantifying morphogenesis in 4D.
- VisiGene – virtual microscope for viewing in situ images
- GIMP – free powerful image editor similar to photoshop.
- CellProfiler – free open source cell analysis software (note: steep learning curve but plenty of video tutorials).
- And on the CellProfiler blog – Quantifying microscopy images: top 10 tips for image acquisition
- The Holden Lab at Newcastle University have a nice online resource page for an introduction to microscopy
- The Aits Lab YouTube channel contains playlists of image analysis tutorials
- Benjamin Nanes’ incredibly useful “How to Create Publication-Quality Figures – A step-by-step guide (using free software!)“
- On Datawrapper’s Chartable Blog, Lisa Charlotte Rost explores what to consider when choosing colours in data visualisation
- On Addgene’s blog, Joachim Goedhart and Marieke Mastop provide A Practical Approach to Choosing the B(right)est Fluorescent Protein
- In the same place, Goedhart explores the available options when GFP lets you down
- Fundamentals of Data Visualisation – on online preview of Claus Wilke’s book
- The Fluorescent Biosensor Database is a repository of the array of fluorescent biosensors developed to study cell signaling in live cells
- Tips for designing figures for color blind readers, from somersault1824
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Travel grants & research tips
Research grants:
- Development travel fellowships to carry out research in a host laboratory – various deadlines throughout the year.
- Genetics society training grant to undergo training in the field of genetics research- applications are reviewed quarterly.
- JSPS fellowships to carry out research at Japanese Universities.
- EMBO short term fellowships for collaborations between research labs.
Funding for undergraduates to get lab experience:
- Various societies, charities and funding bodies offer funding for undergaduates:
- Various UK Institutes have their own programmes:
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- LMS, London
- Oxford Cardiovascular Science
- Lister Institute of Preventive Medicine, London
- Institute of Cancer Research, London
- Francis Crick Institute, London
- Cancer Research UK Cambridge Institute
- MRC Cancer Unit Cambridge
- University of Edinburgh – MRC Institute of Genetics and Molecular Medicine
- Amgen Scholars Program
- University-wide programmes in the UK:
To attend meetings:
- BSDB The Company of Biologists travel grants to attend conferences and workshops – applications reviewed at the end of each month.
- Genetics society junior scientist conference grant – applications are reviewed bi-annually.
- SDB travel awards – various deadlines throughout the year.
- Guarantors of brain travel awards – submit at least 9 weeks before conference start date.
- EMBO travel fellowships to attend meetings.
- EMBO funding to organise conferences and meetings.
Research tips:
- The Wellcome Trust has a useful PDF ‘A career in research – Tips for running your own research group’
- ‘A chalk talk on chalk talks‘ – tips from José Dinneny on this often daunting interview procedure
- ‘Professional Development Opportunities for Research Trainees‘ – A FASEB webinar for research trainees looking to explore career options
- The Johns Hopkins School of Medicine’s Professional Development and Career Office website has resources on career paths, job application materials, professional development opportunities, and more
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Have we missed a useful database? Get in touch!