How can I access cryosparc from home or elsewhere?
When you want to access cryoSPARC from home or elsewhere to be able to run jobs and view results, it can be convenient to connect to the web server via an SSH tunnel. SSH tunneling is a method of transporting arbitrary networking data over an encrypted SSH connection.
How does the cryosparc web interface work?
The cryoSPARC web interface can be accessed from any computer on the same network as the computer running cryoSPARC, meaning that a single desktop computer or rackmount server can provide reconstruction and classification service for an entire group of cryo-EM users who each access the software from their own computers.
How do I connect to the cryosparc master server?
Most institutions offer Virtual Private Network (VPN) capability which can allow you to connect to the institution's local network as if you are physically present at the office. There are different types of VPN connections, but most will allow you, once logged in, to connect to the cryoSPARC master server as you usually would, using your browser.
What port does cryosparc run on?
By default, cryoSPARC user interface pages are served by a web server running on the same master node where cryoSPARC is installed, at port 39000. This web server is responsible for displaying datasets, experiments, streaming real time results, user accounts, updating, etc.
How to connect to a cryoSPARC server?
What port is CryoSPARC installed on?
What is a VPN in a CryoSPARC server?
Where is the master cryoserver?
Does cryosparc require internet?
Can you use SSH to connect to a CryoSPARC?
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How do I access cryoSPARC?
At minimum, cryoSPARC have access to our license server at https://get.cryosparc.com/ . On some older systems, or if your system is behind a HTTP proxy, cryoSPARC may have trouble getting the required SSL certificates to validate this requires.
How do I quit cryoSPARC?
Stopping cryosparc. A cryoSPARC process may have been orphaned. You will have to kill it. Then, delete the unix:///tmp/cryosparc-supervisor-2d5891e41f1cbf50751930c18d4147eb.sock file.
How do I update cryoSPARC?
Checking for updates Log in to the workstation or remote node where cryosparc_master is installed. Use the same non-root UNIX user account that runs the cryoSPARC process and was used to install cryoSPARC. Run all commands on this page in a terminal running bash.
How to Download, Install and Configure - CryoSPARC Guide
Once you've reviewed the cryoSPARC Installation Prerequisites and have decided on an architecture suitable for your situation, the installation process can be distilled to a few main steps:
Connecting worker to master - cryoSPARC Discuss
Attempting to register worker 134.74.27.139 to command 134.74.27.116:39002 Connecting as unix user cryosparc_user Will register using ssh string: cryosparc_user@134.74.27.139 If this is incorrect, you should re-run this command with the flag --sshstr
cryoSPARC | SPA Cryo-EM Software Systems
Get the cryoSPARC™ System. CryoSPARC™ and cryoSPARC Live™ are available free of charge for non-profit academic use.Please fill out the form to request a license. Please allow up to 24 hours for us to respond to your request.
How to add new users in CryoSPARC2? - Tips - cryoSPARC Discuss
Hi, I tried to follow the instruction to add new users. I log out the admin account and looked for a place to add new users. But there is only log in page with input boxes for user name and password, link for Forget Password, a button for Log in, no button or link for Sing Up.
What is cryosparc software?
The cryoSPARC software is available as a standalone program that can run on either commodity desktop workstations or rackmount servers. Once particle images are selected and corrected for anisotropic beam-induced movement 46 and the effects of radiation damage 46, 47, they may be processed through the program's web browser graphical user interface (GUI). At minimum, a single consumer- or professional-grade NVIDIA GPU is required. The easy-to-use GUI ( Supplementary Video 1) provides the same interface for both local and remote usage. This GUI allows multiple users within a laboratory to have separate accounts, access the program remotely, upload and share data sets, manage experimental results, launch computational tasks, and view results streaming in real time as they are computed.
What is cryo EM map?
Cryo-EM map calculation is a nonconvex optimization problem. This type of problem is among the most computationally challenging optimization problems known and is characterized by the presence of multiple locally optimal settings of variables, each of which forms an attractor where typical iterative optimization algorithms can become stuck if poorly initialized 19 ( Fig. 1a ). Sensitivity to local optima is seen in most optimization algorithms, including those used in cryo-EM 12, 13; and, as a result, refinement programs require a reasonably accurate initial model for the structure that initializes the search near the global optimum. Recently, however, methods have been discovered that perform well on nonconvex problems. One such method is SGD 20 ( Fig. 1 ). SGD was popularized as a key tool in deep learning for the optimization of nonconvex functions, and it results in near human-level performance in tasks like image and speech recognition 21, 22.
How to find optimal pose in cryo EM?
3b ), an inexpensive lower bound on the error is first computed across the entire space of poses. At the pose that minimizes this lower bound, the computationally expensive true error function is evaluated. All regions of the search space where the lower bound exceeds this computed value of the true error function cannot contain the optimal pose and can be excluded from further search. A new lower bound is then calculated that fits more tightly to the true error function but is more expensive to calculate. The process of evaluating the error function at the optimum of the lower bound, discarding regions of search space where the true error is above the lower bound, and recalculating a tighter fitting lower bound, is repeated until only the optimal pose remains.
What is the FSC for 3D maps?
In all 3D map refinement experiments, the Fourier shell correlation (FSC) between two independently refined half maps (the 'gold standard') was used to assess resolution 30 along with the FSC = 0.143 resolution criterion 31 and correction of the FSC for effects of masking by high-resolution noise substitution 32.
Is structure determination by cryo-EM an optimization problem?
Formally, structure determination by cryo-EM is an optimization problem and may be described in a Bayesian likelihood framework 12, 17:
Can SGD be used to map homogeneous data?
We previously showed that SGD could produce a reasonable low-resolution map ab initio for a homogenous data set 42. Here we have demonstrated that SGD is sufficiently robust to enable reconstruction of multiple 3D classes from independent arbitrary initializations. To our knowledge, all existing techniques for 3D classification use a single initial reference from which analysis of heterogeneity proceeds. Removal of the assumption that all 3D classes are similar to the single input reference is particularly advantageous for discovering 3D states that are unexpected and different from the consensus structure. It is important to note that, like other algorithms, SGD will fail when the particle images do not contain a sufficient series of views to define the 3D structure of the molecule. It can also fail if there are sufficient views but strongly preferred orientations for particles. Other pathological situations may include analysis of data sets with little contrast at low resolution. This situation can occur when insufficient defocus is used with a cryo-EM microscope that does not possess a phase plate or when imaging low-molecular-weight complexes.
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How to connect to a cryoSPARC server?
You connect to this server normally from within your institution network by using your browser and pointing to the correct URL. For example, say you work at an institution with domain myuniversity.com. If you have installed the cryoSPARC master application on a machine that has a hostname of uoft on your local network you can usually access this as http://uoft:39000 or http://uoft.myuniversity.com:39000
What port is CryoSPARC installed on?
By default, cryoSPARC user interface pages are served by a web server running on the same master node where cryoSPARC is installed, at port 39000. This web server is responsible for displaying datasets, experiments, streaming real time results, user accounts, updating, etc.
What is a VPN in a CryoSPARC server?
Most institutions offer Virtual Private Network (VPN) capability which can allow you to connect to the institution's local network as if you are physically present at the office. There are different types of VPN connections, but most will allow you, once logged in, to connect to the cryoSPARC master server as you usually would, using your browser.
Where is the master cryoserver?
Often, the master cryoSPARC server may be behind a firewall, within a local network (LAN) at your institution. Only other machines that are on the same local network can connect to the master server at port 39000.
Does cryosparc require internet?
cryoSPARC requires internet access from the main process to verify your license and perform updates. At minimum, cryoSPARC have access to our license server at https://get.cryosparc.com/.
Can you use SSH to connect to a CryoSPARC?
If you can use SSH to connect to the cryoSPARC master instance, you can run an SSH command to forward the port of your remote instance to your local machine. Start an SSH tunnel to expose a port (by default, 39000) from your master node to your local machine.
