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.
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!). Plus some collected research tips.
Species resources and databases
Avianbase – genome sequence and annotation for 44 bird species.
GEISHA – chick expression data for first six days of development.
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.
H-InvDB – human genes and transcripts.
HUDSEN – 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.
MBase – Medaka Genome Database.
4D Atlas of mouse development (E11.5 – E14).
DMDD – high-resolution images and phenotype data for embryos and placentas from embryonic-lethal lines.
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.
Mouse Genome Informatics (MGI) – integrated gene expression, phenotype, and gene ontology annotations for mouse genes, as well as complete gene and allele catalogs.
ZMP – Zebrafish Mutation Project.
AgBase – curated resource for functional analysis of agricultural plant and animal gene products.
Fourmidable – ant genomics database.
Drosophila Network resources – full list of Drosophila resources, curated by FlyBase.
EchinoBase – echinoderm genomic database.
Caenorhabditis Genetics Center (CGC) – stock centre.
WormAtlas – Database of behavioral and structural anatomy of C. elegans.
GDR – Genome Database for Rosaceae.
Gramene – comparative genome analysis of grasses.
Dendrome – forest tree genome database.
Facebase – craniofacial development and malformation.
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.
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.
- 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
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
- 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
Travel grants & research tips
To do research:
- Gurdon studentships to allow undergraduates to carry out summer lab projects – application deadline end of March.
- 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.
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.
- 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
Have we missed a useful database? Get in touch!