reCOGnizer
Ory Keto
reCOGnizer | Ory Keto | |
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9 | 35 | |
26 | 4,618 | |
- | 1.1% | |
7.4 | 8.5 | |
4 months ago | 7 days ago | |
HTML | Go | |
BSD 3-clause "New" or "Revised" License | Apache License 2.0 |
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reCOGnizer
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Is there a way to achieve a similar COG annotation for Haloferax mediterranei?
reCOGnizer (https://github.com/iquasere/reCOGnizer) will do that for you. It also outputs the COG categories in a krona plot
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Why do some HMMs come with a separate score table instead of embedding in as cut_ga, cut_tc, or cut_nc?
What tool are you using for analyzing them? Using something like reCOGnizer (https://github.com/iquasere/reCOGnizer) gives you the bitscores and evalues in a TSV table, next to the matches
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Metadbgwas, my tool ! What could I do better ?
Finally, a huge help on developing is having a Continuous Integration/Deployment on the tool. CD refers to the conda suggestion above, as your tool would be readily available in a controlled environment. CI could use the GitHub Actions functionality provided by GitHub. You can see an example here
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Any programs/packages that will allow me to compare cluster annotations obtained from metagenomic data?
You may run MOSCA (https://github.com/iquasere/MOSCA), it performs all major steps of metagenomics analysis. It includes that functional classification you are looking for, since with UPIMAPI (https://github.com/iquasere/UPIMAPI) it annotates with UniProt DB as reference, and obtains information including taxonomy, EC numbers, and even those GOs, and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotates with CDD DB as reference, and obtains orthologous groups information (COG, Pfam, etc).
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Metatranscriptomics Workflow Questions?
Prediction of coding sequences takes as input the contigs you obtained, and gives you the translated genes. Besides annotating with the KEGG database, you may also want to annotate with more general purpose databases (e.g. UniProt), as these provide more taxonomies and functional information. MOSCA includes UPIMAPI (https://github.com/iquasere/UPIMAPI) and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotate genes with reference to UniProt and CDD databases using two different methods, providing complementary information. This is the same methodology used by widely popular tools such as eggNOG-mapper and Prokka, but these use other databases.
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Problems using Prokka
Install with mamba instead of conda, no more problems. Or use UPIMAPI (https://github.com/iquasere/UPIMAPI) together with reCOGnizer (https://github.com/iquasere/reCOGnizer), since these tools obtain better results when annotating proteins
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How would you name the program that does cog annotation?
I think reCOGnizer is a nice name
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
reCOGnizer (https://github.com/iquasere/reCOGnizer) can annotate with COGs, and the other databases available at CDD. It obtains all information concerning COGs description and categories, and outputs krona plots and TSV tables in formats easy to analyze. There is also mantis (https://github.com/PedroMTQ/mantis), prokka (https://github.com/tseemann/prokka) and DFAST (https://github.com/nigyta/dfast_core), the latter two work on contigs and the first two are for proteins
Ory Keto
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Show HN: Blueprint for a distributed multi-region IAM with Go and CockroachDB
One of Ory’s core competencies is permissions. We built the first Google Zanzibar implementation in the world and it’s part of Ory Network‘s global multi-region platform (https://github.com/ory/keto)
A push model is also valid if you’re heavy on policies and can accept eventual consistency. We will investigate how to generally push things to the edge (like we did with Ory Edge Sessions) or to cryptographic verification wherever staleness is acceptable.
By solving the primitives correctly in the beginning (with a multi region architecture) that job does become a lot easier, which is what we decided doing at Ory :)
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Show HN: Open-source IAM Ory Kratos v1.0 with Passkeys, MFA and multi-region
slightly off-topic, but related to what ory is doing in general. How do you usually do authorization-aware search?
Imagine, I have a bunch of Google docs and using https://github.com/ory/keto for authorization. I can quickly answer the question "does user X have access to document Y", but it is not easy to do "search all documents with word Hello in it, for which I have access" because access can be granted through nested groups (give read access to everyone in DepartmentA, and I am part of child department)
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how to design database for Access Control Privileges ?
if you want to integrate an existing framework see if https://github.com/ory/keto solves your problems, there are similiar frameworks that support ABAC
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Understanding Google Zanzibar and Why Shines at Building Permissions
Shameless plug for Ory Keto, probably the best reference implementation IMO https://github.com/ory/keto
- We built an open source authorization service based on Google Zanzibar
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Open-source authorization service and policy engine based on Google Zanzibar
Looks cool, wonder how it compares to Keto and Casbin.
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Launch HN: Warrant (YC S21) – Authorization and access control as a service
How does Warrant compare to other Zanzibar based solutions like Ory Keto ?https://github.com/ory/keto
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Show HN: Open-source authorization service based on Google-Zanzibar
Interesting to see another project open sourced around Google Zanzibar. On a timeline for context:
- Ory came out first with Ory Keto ( https://github.com/ory/keto ) which is trying to be a close adaptation of the paper. Initially, many concepts were missing but they are making a lot of progress with the DSL and it interfaces with the rest of Ory (OAuth2, User Mangement)
- Authzed came out as a SaaS only, open sorucing the code base later on at https://github.com/authzed/spicedb
- Auth0 has been playing around with Zanzibar concepts in various forms and published a beta service at https://dashboard.fga.dev - apparently now also open source parts of it similar to what Authzed did: https://github.com/openfga
- Permify - who on a side note spammed me quite a lot with outreach because I was active in these communities - joins as well https://github.com/Permify/permify
It's exciting to see so much movement, yet also sad that so many companies are brewing their own beer instead of working collaborative on the more succesful projects. Feels like we'll just end up with one or two successful projects (looking at Ory / Auth0 here) with the rest perishing. I'm wondering if there truly is a business model for just this permission system as a saas service (looks like this is what everyone is going with). Here I'm giving Auth0 probably the biggest plus as they have an established identity service. Then again, Okta (parent of Auth0) and Auth0 themselves are not particularly known for good business practices that we usually expect from developer tooling.
What's refreshing though with Permify is that they are trying a bit of a different approach to Zanzibar!
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Zanzibar-like authorization framework written in Go
Er, Ory Keto is written in Go.
What are some alternatives?
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
OPA (Open Policy Agent) - Open Policy Agent (OPA) is an open source, general-purpose policy engine.
orfipy - Fast and flexible ORF finder
spicedb - Open Source, Google Zanzibar-inspired permissions database to enable fine-grained access control for customer applications
guardian_db - Guardian DB integration for tracking tokens and ensuring logout cannot be replayed.
casbin - An authorization library that supports access control models like ACL, RBAC, ABAC in Golang: https://discord.gg/S5UjpzGZjN
pyfaidx - Efficient pythonic random access to fasta subsequences
Keycloak - Open Source Identity and Access Management For Modern Applications and Services
progen - Official release of the ProGen models
cerbos - Cerbos is the open core, language-agnostic, scalable authorization solution that makes user permissions and authorization simple to implement and manage by writing context-aware access control policies for your application resources.
Ory Kratos - Next-gen identity server replacing your Auth0, Okta, Firebase with hardened security and PassKeys, SMS, OIDC, Social Sign In, MFA, FIDO, TOTP and OTP, WebAuthn, passwordless and much more. Golang, headless, API-first. Available as a worry-free SaaS with the fairest pricing on the market!
oso - Oso is a batteries-included framework for building authorization in your application.