General Toolkit

• https://www.onezoom.org/

  • I use this frequently to find the rough date of the the last common ancestor (LCA, relative to humans) of organisms I am learning about.

• https://timetree.org/

  • Awesome tool for generating publication quality phylogenetic trees. 

• https://reporter.nih.gov/advanced-search

  • Looking for jobs in academic labs? Might want to check their funding situation first!

• https://www.payscale.com/cost-of-living-calculator

  • Moving to a new city on a tech, grad student, or postdoc salary? Might want to check how far your cash will take you. 

Behavioral Analysis Toolkit

• https://sleap.ai/

  • My go-to GPU-based tracking software. I much prefer this interface over DLC due to it's human in the loop training features, fast training times with loss-plateu cut-offs,  and easy to use skeleton  drawing features. Love this software!

  • Click here for my protocol [in active development]

• https://goldenneurolab.com/simba

  • From Simon Nilsson and Sam Golden's Lab at UW, this software is another go-to for me for analyzing SLEAP and DLC output data files for movement dynamics, time spent in ROIs, and supervised and unsupervised behavioral classifiers. 

  • Click here for my protocol [in active development]

• https://janclemenslab.org/das/index.html

  • A truly remarkable piece of software for segmenting out mouse ultrasonic vocalizations (or really, any "sound") from audio data. Deep neural network based approach, with a lightweight and fairly easy to learn GUI. Python based, and so open-source. Replaced DeepSqueak for my analysis. 

  • Click here for my protocol [in active development]

• https://github.com/DeepLabCut/DeepLabCut

  • Not my go-to, but still a solid piece of software that is used broadly by the neuroscience and behavior community. It changed the game when it came out!

• https://sourceforge.net/projects/toxtrac/

  • A stand-alone CPU-based multi-animal tracking software with a relatively simple GUI and ROI analysis capability. Best for videos of a single animal with a simple background or of low numbers of animals with no occlusions. Great for simple behavior tracking projects for undergrads who want to track short videos on their laptops (also pretty good in a classroom setting). 

• https://idtrackerai.readthedocs.io/en/latest/

  • An older machine learning based tracker. The first I ever used!

• https://github.com/swarm-lab/trackR

  • An R-based 'classical' tracking program using OpenCV. Great for simple projects and for those new to programming/software generally.

• https://github.com/DrCoffey/DeepSqueak

  • My previous go-to for USV detection analysis in mice. Feature rich, but purely MATLAB-based. 

Neuroscience Toolkit

• https://brainmuseum.org/

  • Comparative brain anatomy across a variety of taxa with downloadable images, stains, slices, etc. 

• http://labs.gaidi.ca/mouse-brain-atlas/

  • Big shout out to Dr. Matt Gaidica for putting this out in the world. I use it all the time to check my stereotaxic surgery targeting. 

• https://ebrains.eu/services/atlases/

  • EU based brain atlases and other services. Nice 3D models here and GUI, especially if you check out via the siibra-explorer. 

• http://atlas.brain-map.org/

  • Allen Institute Brain Atlas, 3D and coronal slices available. 

• https://observatory.brain-map.org/visualcoding/

  • Allen Institute Brain Observatory data

• http://braininfo.rprc.washington.edu/Default.aspx

  • Nice site for quickly referencing unfamiliar brain regions. A bit outdated, but still useful! Links to the Allen toolkits for data. In some ways the GUI is more intuitive than the Allen interface!

• https://cic.ini.usc.edu/

  • Mouse Connectome Project from Larry Swanson's group at USC (and others). 

• https://sites.google.com/view/the-neurome-project/home

  • The Neurome Project from Larry Swanson

• https://mouselight.janelia.org/

  • From the folks at Janelia, you can use this to see the morphology of entire neurons across a 3D model of the brain. 

• https://neuprint.janelia.org/

  • From Janelia, drosophila connectomics explorer. Can also look at electron microscopy data. 

  • What can we learn about the Deep homology between vertebrates and invertebrates. 

  • Define cell types by connectivity, and neurotransmiters and other features. All trained via machine vision. Born from major research collaboration with google (and others)

• https://biccn.org/

  • NIH Brain Initiative Cell Census Network imaging and genomic data sets. 

• https://alphafold.ebi.ac.uk/

  • From the folks at DeepMind, great tool for checking the structure of proteins of interest. 

AI Toolkit

• https://elicit.org/

  • Fantastic tool for asking questions about what is known within a given research area and finding relevant literature.

• https://chat.openai.com/chat

  • Simply an invaluable tool for coding/programming. 

• https://rtutor.ai/

  • I typically use ChatGPT directly, but I have found this occasionally useful. 

• https://labs.openai.com/

  • OpenAI's DALL-E. I have used to create various images and cartoons for talks, quite helpful, although there are other competitors out there (i.e. Midjourney and a host of AI-"art" apps).

• https://stablediffusionweb.com/

• https://microscope.openai.com/models

  • For visualizing neural network models/layers.

PI Level Funding

• Brain Research Foundation Scientific Innovations Award

Postdoc Level Funding (early stage, apply before or during ~first year)

• General list servs tracking postdoc fellowships

  • Funding Opportunities for Postdoctoral Scholars | FAS Research Administration Services

  • Funding Opportunities | VPR at JHU

• NSF PRFB Postdoctoral Research Fellowships in Biology (PRFB)

  • One can apply up to 15 months after graduation. The PRFB, more so than other fellowships, typically is funding a particular project as opposed to a person, so the aims of the fellowship should be “completed” even if one were to transfer the fellowship to a new institution. 

• NIH F32/NRSA/Ruth L. Kirschstein Individual Fellowships

• Schmidt Science Fellows

• Life Sciences Research Foundation 

• James Coffin Childs Memorial Fund for Medical Research Postdoctoral Fellowship

• Helen Hay Whitney Fellows

• Human Frontier Science Program Postdoctoral Fellowship

• National Geographic Society

• Harvard Postdoctoral Fellow Award | Mind Brain Behavior

• Harvard Junior Fellows

• University of Michigan Society Fellows

• UC Berkeley Kathryn Miller Postdoctoral Fellowship

• Cornell Klarman Fellowships

• Stanford Science Fellows

• UT Austin Stengl-Wyer Scholars Program

• NYU Provost's Postdoctoral Fellowship Program

• Brain & Behavior Research Foundation

• DARPA Innovation Postdoctoral Fellowship

• Army Research Laboratory Distinguished Postdoctoral Fellowship

• Air Force Science & Technology Fellowship Program

• Klingenstein-simons Postdoctoral Fellowship award in neuroscience

• Alfred P. Sloan Research Fellowship

• DFG Post-Doc Fellowship (Germany)

• Grass Foundation Rising Stars Award

• The Branco Weiss Fellowship – Society in Science

• EMBO Postdoctoral Fellowship

• NSF Biodiversity Postdoctoral Fellowship

• Rita Levi-Montalcini Postdoctoral Fellowship

• Cornell Presidents Fellowship

Postdoc Level Funding (late stage, pathway to independence)

• NIH K99/R00 Pathway to Independence Award

• Simons Foundation Autism Research Initiative (SFARI)

• Simons Foundation Collaboration on the Global Brain (SCGB)

• Simons Collaboration on Plasticity and the Aging Brain (SCPAB)

PhD Level Funding

• NSF GRFP

• NDSEG

• HHMI Gilliam Fellows Program

Undergraduate Level Funding

• Beckman Scholars Program

Any Level Funding

• ARPA-H Program Manager

• Ford Foundation Fellowships (Pre-doc, Doc, Postdoc, Senior)