FAQ
Q:How to open a session in Delta.AR?
A: Firstly, you should open the application Delta_AR in HoloLens Headset, a session id will be shown. Then input the session id in the AR configuration web page.
Q:How to add a track into HoloLens?
A:In Genome View and Topological View, click the shown track to active a pop-up dialog box, find the checkbox called "Shown in Delta.AR ", then check. The track will be added into the HoloLens view
Q:Can I interactive with Genome View?
A: Yes. In Hololens, you can choose one ball or choose one interaction by using Air-Tap gesture
Q:How HoloLens view communicate with 2D device?
A: The whole Delta.AR system is designed as M(Model)-V(View)-C(Control) style, a custom structure of J2EE that can easily be maintained and extended. Two events are defined in HoloLens that support selecting a ball or highlighting an interaction loop. The events in HoloLens will trigger the active data synchronization between HoloLens and web server, in turn signaling the portable device to update the genome browser. The events in genome browser will trigger active data synchronization between the portable device and web server, in turn signaling HoloLens to update the hologram. All epigenetic annotation data and 3D physical models are maintained in a MySQL database. The installation package can be downloaded from http://deltaar.big.ac.cn/deltaar/pages/download/download.jsp. A video tutorial is available for the installation at this page.
A simple application layer protocol (AALP) for communication among HoloLens, portable device and data source. AALP is an HTTP-based interface for data exchange. The link from HoloLens and portable device to data source is defined as the uplink, while the reverse link is defined as the downlink. The connection is established through the web server for http://deltaar.big.ac.cn. Two JSON files are found on the web server. One maintains the parameters of HoloLens (JSON.Hololens), and the other maintains the genome browser parameters in the portable device (JSON.Portable). JSON.Hololens and JSON.Portable are monitored by the portable device and HoloLens, respectively. When the Delta.AR app is launched in HoloLens, a session ID is assigned. By inputting this session ID to the server through the webpage, a communication session between the HoloLens and the webserver is established, and any further data exchanges will be conducted by this session ID.
1. Uplink from HoloLens/portable device to the data source. A HoloLens event, e.g., selecting an interaction in HoloLens, triggers an uplink communication. The parameters of this event are saved to JSON.Hololens.
2. Downlink from data source to the portable device. The genome browser in the portable device monitors the updating of JSON.Hololens and refreshes the genome view in the browser accordingly.
3. Downlink form data source to HoloLens. HoloLens monitors the updating of JSON.Portable and updates the current hologram accordingly. Parameters in JSON.Hololens.
Example:
[{"annotation":{"currentTrack":"Interaction,TAD,LCR_Gene,K562_EZH2","event":""},"hololens":{"hololensid":"0045"},"model":{"bin":"50000","chrom":"11","end":"6500000","name":"3dmodel","organism":"hg19","start":"4500000"},"portal":{"jobId":"hg19"}}], where
Annotation: the annotated tracks
CurrentTrack: currently viewed annotated tracks
Event: name of the event
HoloLens: the identification of HoloLens
Hololensid: the session ID, as shown in HoloLens
Model: physical 3D model information
Bin: bin size for 3D model
Chrom: chromosome of genomic region
End: end position of genomic region
Name: name of 3D model
Organism: name of organism
Start: start position of genomic region
Portal: identification of genome for web portal
jobId: genome identification
4. Parameters in JSON.Portable.
Example:
[{"annotation":{"currentTrack":"Interaction,TAD,LCR_Gene_signal,K562_EZH2_signal","event":"select_region"},"hololens":{"hololensid":"0045"},"model":{"binStart":"90","loc":"11:5900000..5950000","organism":"hg19","resolution":"50000"}}], where
Annotation: the annotated track
CurrentTrack: currently viewed annotated track
Event: name of the event in HoloLens
HoloLens: identification of HoloLens
Hololensid: session ID, as shown in HoloLens
Model: physical 3D model information
binStart: genomic start position mapped in 3D model
Loc: genome coordinate
Organism: name of organism
Resolution: binsize of 3D model
A simple application layer protocol (AALP) for communication among HoloLens, portable device and data source. AALP is an HTTP-based interface for data exchange. The link from HoloLens and portable device to data source is defined as the uplink, while the reverse link is defined as the downlink. The connection is established through the web server for http://deltaar.big.ac.cn. Two JSON files are found on the web server. One maintains the parameters of HoloLens (JSON.Hololens), and the other maintains the genome browser parameters in the portable device (JSON.Portable). JSON.Hololens and JSON.Portable are monitored by the portable device and HoloLens, respectively. When the Delta.AR app is launched in HoloLens, a session ID is assigned. By inputting this session ID to the server through the webpage, a communication session between the HoloLens and the webserver is established, and any further data exchanges will be conducted by this session ID.
1. Uplink from HoloLens/portable device to the data source. A HoloLens event, e.g., selecting an interaction in HoloLens, triggers an uplink communication. The parameters of this event are saved to JSON.Hololens.
2. Downlink from data source to the portable device. The genome browser in the portable device monitors the updating of JSON.Hololens and refreshes the genome view in the browser accordingly.
3. Downlink form data source to HoloLens. HoloLens monitors the updating of JSON.Portable and updates the current hologram accordingly. Parameters in JSON.Hololens.
Example:
[{"annotation":{"currentTrack":"Interaction,TAD,LCR_Gene,K562_EZH2","event":""},"hololens":{"hololensid":"0045"},"model":{"bin":"50000","chrom":"11","end":"6500000","name":"3dmodel","organism":"hg19","start":"4500000"},"portal":{"jobId":"hg19"}}], where
Annotation: the annotated tracks
CurrentTrack: currently viewed annotated tracks
Event: name of the event
HoloLens: the identification of HoloLens
Hololensid: the session ID, as shown in HoloLens
Model: physical 3D model information
Bin: bin size for 3D model
Chrom: chromosome of genomic region
End: end position of genomic region
Name: name of 3D model
Organism: name of organism
Start: start position of genomic region
Portal: identification of genome for web portal
jobId: genome identification
4. Parameters in JSON.Portable.
Example:
[{"annotation":{"currentTrack":"Interaction,TAD,LCR_Gene_signal,K562_EZH2_signal","event":"select_region"},"hololens":{"hololensid":"0045"},"model":{"binStart":"90","loc":"11:5900000..5950000","organism":"hg19","resolution":"50000"}}], where
Annotation: the annotated track
CurrentTrack: currently viewed annotated track
Event: name of the event in HoloLens
HoloLens: identification of HoloLens
Hololensid: session ID, as shown in HoloLens
Model: physical 3D model information
binStart: genomic start position mapped in 3D model
Loc: genome coordinate
Organism: name of organism
Resolution: binsize of 3D model